@lbruun Hi Laura. I’m sorry to learn of your your current issue with the software.
I’ll reply from two P.O.V’s One as a Pencil2D team support mod, and another one as an animator myself.
Support POV
Pencil2D losing frames randomly (Potential causes & solutions)
First off it’s important to explain that this is not a simple Pencil2D bug. And this doesn’t happen to everyone.
Most reports we have got in the last few years in regards to this, are related to third party apps, or even the same operating system, wiping clean the operating system’s %TEMP% (or temporary files) folder which Pencil2D uses to deploy the open document on any given work session.
Basically When you create a new file in Pencil2D or open an existing file. All the Project folder contents will be dumped into the temporary files folder so the software can work off them easily.
Once you save a file it will take the same folder and package it into the “save file” you name and locate somewhere else.
So what happens is that for reasons that we can’t control (at least so far), the files are getting deleted by a third party (that is, not by you, not by Pencil2D) in the temp folder.
Once the files are deleted, the reference that exists in your Pencil2D document, will still be kept, but it will be pointing to a non-existent image. In this case when you save the work back to the actual file, you’re saving basically empty frames back into the file, because the app can’t locate the image resources, but since the actual frame containers are still created (and probably cached on the RAM or computer memory) that’s why it gives the illusion that the project is still functional so it’s harder to notice during the actual work and until you open the file again.
While you may or may not have a 3rd party app that does this, it is the most likely related issue.
For example we had another user whose work mimics pixel art game animation, so they had to import a lot of image resource, and used to have this problem A LOT. My recommendation to them Is the same I’ll give to you as follows:
-
Never save over the same file thrice. Seems a bit extreme but this applies to commercial software like Toonboom Harmony or Adoble Animate which use similar text-based files to save references to the actual drawing resources.
Quite frankly file save overwrites can get to a point where text files being modified will become corrupted or messed up after saving too many times, so it’s up to us, the artists, to have a habit of saving backup files.
That doesn’t mean Pencil2D shouldn’t assist in this process, and we are looking into having at some point a backup system for animation files, but we’re not on that timeline yet 
-
I always recommend to either save numbered files e.g my_animation_001.pclx or use a file versioning system (FVS).
Windows has one called File History embed, but I personally have used SVN and GIT which are made for programmers, but can be easily used by artists to keep a personal, chronological record of your file changes (at least if you’re disciplined enough)
-
Save the project as a Project Folder instead of a Project Package: Pencil2D has two types of save files:
- The *.PCL file format (Project Folder)
- The *.PCLX file format (Project Package)
Saving as a *.PCL will save the original project folder with all the actual elements you drew and imported inside a .data folder within a location of your choice (e.g desktop)
This is similar to how professional apps work like Toonboom Harmony (saves to a project folder by default), or even Adobe Animate, with their XFL file format.
The advantage of this is that it works really well with a FVS, and you can edit the image resources directly with other apps for quick edits.
The apparent downside (since I’m not entirely sure) is that if the app crashes you might not have access to the primitive crash recovery system we currently have (but I’ll have to confirm that later).
Other than that most issues related to the TEMP folder should be addressed with this method
-
Regarding file corruption we have a dedicated guide to handle this.
Most of the tips and procedures could help recover work that should be locked by a corrupted file, but 90% of the time ppl have to redraw the artwork like you already did.
Animator POV
Workflow considerations
First I’ll discuss some workflow tips from a personal position, not as a Pencil2D forum mod but as a professional animator.
To be honest there are many hints in your text that tell me that you might be working on a project that is bigger than what it’s expected from regular Pencil2D users to create. And in that sense I can only applaud your mettle and dedication 
In such case, it’s of course not only the responsibility of the tool but also the user to look for a better workflow, regardless of the tool.
My personal advice as an animator is the following:
- Never create an animation longer than a single shot length using any software. Always work in scenes or shots per file and then string them together using a video editing software. This is how it’s done in professional settings.
- Never save the same animation for a long period of time on a single file. Save numbered or versioned files as often as possible for each minor or major milestone. Commercial software also breaks and corrupts files, so I always save my files like
MyAnimation_0001.(xxx)
I’ve had my fair share of issues with Toonboom Harmony, TVPaint and Adobe Animate CC on paid projects where recovery was impossible and versioned backups saved my team’s work
- Make backup copies that won’t be overwritten or saved over This goes in hand with #2, but it’s different to have an emergency copy to continue saving over, than having a separate backup copy that won’t be touched by anyone, including yourself.
A clean backup of your work should be copied and then opened as a copy, so you won’t write over the backup after new progress. that way in case something breaks you can go back to it and reimport missing parts like you already did.
- If the tool doesn’t work, find out why and how it’s breaking for you, then report the issues to the developer team.
If the developer team of a particular tool can’t fix your issue or is unavailable (like in commercial software) then change tools to be able to finish the job for delivery. Period.
This might sound counter intuitive, and I’m sure it might be expected of me to ask you to keep using Pencil2D, but we are not A-d-o-b-e trying to sell you yearly subs. We do this because we want people to do their work better, but it’s not always easy to keep the software working perfectly.
Pencil2D is an open-source software maintained by unpaid volunteers, so while we are eager to help and fix issues, it might be impossible to fix problems that depend on the operating system or third party tools when we can’t replicate it. But that doesn’t mean you have to resign yourself to keep using the app if it keeps failing!
If the workarounds I provided in the explanation at the start of the reply simply do not work, then take the animation you have, export each layer as a PNG Image Sequence (so you preserve transparency of lineart and colored parts, and then import it back into a different app.
Since you’re about to finish the project, it might be less stressful to learn a new app reluctantly and finish for delivery than to struggle through using the old software with the risk of losing all the work. Of course this is only my personal opinion.
Pencil2D has an alternative software article that should help finding a decent tool to finish your work in the worst case scenario.
From that list, for relative simplicity vs. features you need coming from Pencil2D, I recommend Krita since you would be able to import the image sequences as separate layers and finish the job. You might need a bit of a powerful computer, but I think it shouldn’t compromise your work further.
Let us know later what works and what doesn’t. Take care.
and I really hope I’m misunderstanding this but if I’m not, it would mean you accidentally had your newer file overwrite the backup file… 
