@JacobZeier1992 In the past a clean-up drawing was still an animation drawing that needed to be tracked in the production. If the original key or inbetween had a number, it was meant to keep it. This was only removed when tracing the lineart over to acetate cels, to my knowledge.
In the digital age this can vary however it makes sense to remove it before coloring altogether. Just do it during clean-up or lineart tracing.
As a side note, In some devilishly “quick & dirty” productions it can even reach the compositing stage before it’s removed, but usually these are more experimental or painterly films where the compositing artist has to fix all the mess surrounding (or embedded on) the painted canvas (I’ve had to do this 
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For automatic tracing & efficient coloring just use opentoonz. It’s honestly the best open tool for that right now. Watch this tutorial playlist and imagine Pencil2D is the actual paper animation you would “scan” into your computer, the other steps (including GTS for Windows) are the same.