The original issue was that the color fill would degrade the lines destroying the original lineart. This issue has been improved. The Fill tool now has a color tolerance slider to control how much “feathering” is applied when filling shapes.
If anyone continues to have issues with this please try using nightly builds which are always publicly available at https://www.pencil2d.org/download/#nightlybuild
Here’s a direct link to the latest ones for each major system:
- Windows (7+ | x64bits) https://drive.google.com/open?id=1i1gQRE4En5YMKvU44Hkyt-cTiTy__M2k
- macOS (10.11+) https://drive.google.com/open?id=16M8BkbeNpCxhRuoUwYSkQgyZ9uvRga5e
- Linux (AppImage) https://drive.google.com/open?id=17jHH9rjyHVlzntqTZ-0Z7819AobCnxON
I’m closing this issue as solved.