It sounds a little like document corruption.
There’s no reason you shouldn’t be able to export your doc to PDF — Line Numbers just adds a text frames alongside the main frames with numbers in them, and there’s nothing there that could cause PDF export to fail.
You could try exporting to .idml to see if that fixes things.
Regarding Line Numbers using the Basic object style, what I would do in such a case is delete all the things that Line Numbers has created, and then run it again, so it can rebuild them. This would include the Line Numbers layer (in the Layers panel), and the ScriptLineNumbers object style and paragraph style.
Does any of that help?