IPA (of enough concentration) is the same thing you'd use to clean the circuitry/hardware so it shouldn't cause any damage unless it dissolves with the glue and somehow that's damaging (it shouldn't be).
FreeCAD is probably what you're looking for, it had a bad UI but just released 1.0 recently and is pretty decent now. Also I really recommend checking Pixelorama over libresprite for a FOSS pixel art tool.
IPA (of enough concentration) is the same thing you'd use to clean the circuitry/hardware so it shouldn't cause any damage unless it dissolves with the glue and somehow that's damaging (it shouldn't be).