File won't change increment setting no matter what

Sounds similar to an old problem when using Web and Video based files. Since there is no such thing as a half pixel line, it would not allow you to use it to define a stroke. 

Kate,

Just like the preferences, a single AI document can become corrupt. The corruption can (also) be in some of the artwork, so you may have to recreate some.

The solution is to create a new document and move the artwork into that by copying and pasting into the same place and stacking order, Ctrl/Cmd+C in the ailing document, then Ctrl/Cmd+F or B (front or back)) in the new one, and see whether everything works.

You can work from the top or bottom of the Layers panel and start with whole Layers (if more than one), and in each Layer you can start by selecting everything (Ctrl/Cmd+A with nothing locked/hidden) and trying to move everything over in one go, and see.

Failing that you can try to divide the artwork into part, and see whether things work before the next part.

In this way you will hopefully soon have a working document with all or most of the artwork.