So, I just finished an animation which I created at camera size 100x100. I did this because I like the way the aliased pen looks, with it’s pixelated roughness. However, on trying to export my work, I quickly realized there was no way to preserve the quality of the video. I understand that it won’t be possible to salvage that animation, but for the future: is there any way to preserve the pixelated look that I love about small camera sizes, while still animating in a resolution that will actually work?
Your initial approach was actually the best way to go about making pixel art. You can and should use a small canvas size. The real issue is that currently Pencil2D does not allow you to specify the scaling algorithm if you want to scale the output video. What you can do to “salvage” your existing animation and make new ones is to export the animation at the same resolution as the camera, and then upscale it with an image/video editor that supports nearest neighbour interpolation.
You can also look to other animation programs. I know there are a couple that are more geared towards pixel art. Piskel, Pixel-o-rama, Libresprite, and Asesprite have all been brought up before in similar conversations. Some of these may be able to be used just to do the upscaling previously mentioned too.