Long story short, there's a lot of XML-style tags embedded in the original Word doc(about 3500 of them). The relevant part of the other program reads these tags, then allows us to check off boxes saying which sections we want to keep and which we want to remove. If a section isn't checked off, it'll cut out the section from <Begin Section> to <End Section>. Otherwise, it'll strip the tags away and keep the text inside them.

The problems are always cropping up after a section is removed. If I had to guess I'd wager that a formatting definition is inside the removed text and that it's being removed, so Word is reverting to the default formats, but that's just a guess from my general computer knowledge, and I don't have enough understanding of the intricacies of Word formatting to feel confident that I have it right.