Formatting problems with large files

I have a 300 page novel and about 80-90% of the time when changing format (i.e., italics) on a section or even one line, the entire document is affected. I can go to "Undo" which eliminates the main issue but residual issues remain (i.e., several italicized areas reverted, header/footers altered, line spacing (single spaced for quotes) altered, etc.

Online chat/support says they have no idea...and suggested I try y'all. This only happens since I combined all the files for final submission. No problem of course if no changes are discovered after consolidating...but there are always changes...I have heard of this problem from others...but no solutions...Can you help?