My team and I came across a strange situation. We had a .docx file which we imported and analyze files showed 6391 words. We forgot to remove a single word in the header so we went in and deleted the header and also decided to change the font size from Times New Roman 12pt to Times New Roman 10pt. After making those two changes we reimported and the word count changed to 3902. The segment counts were the same minus the deleted header segment. The content in the segments was also the same. We reversed the font change and imported again and then got the 6391 word count. Then we created one version with 12pt font and one version with 10pt font and imported both in the same project with the same memory, the file word counts showed the 12pt file as 6391 and the 10pt file as 3902.
Naturally this put our team into a panic and we tried the experiment on several files that we had previously imported but luckily, the word counts didn't change.
Unfortunately we cannot share the file here but please comment if anyone has come across this situation before or has some insight to what is going on.
I would check that changing the font size didn't also change the style being used somewhere. I'm wondering if a non-translatable style was introduced in the way you changed the font... or something like that?
It's a shame you can't provide a file that does this! Very interesting.