why are sections deleted automatically?!

Help! It’s causing major problems that sections of documents are marked by track changes as deleted when no one has actually deleted- It has caused major misunderstandings and difficulties and I have had to go through Long documents undoing delete on hundreds of paragraphs-there are some changes I need to leave so I can’t just do reject all- really frustrating and not an option in the long run.
The documents have been sent to others using Word and back again a few times- is that a problem? would be Very grateful for Any adivce!