FWIW, this morning I saw what appeared to this problem in Mail Version 12.4 (3445.104.14) on macOS 10.14.6 (18G5033) Mojave.
In Trash, I have an On My Mac folder. In that folder, I have messages from Lending Tree. (Aside: I never even visited Lending Tree’s web site and I don’t know where it got my email address, but I get a message or two each month. I move said messages to this folder.) There are three messages from entities other than Lending Tree in this On My Mac folder. This morning, I received a Lending Tree message, and for no reason in particular, I opened an earlier message. The body was missing.
The three other messages, all older than the oldest Lending Tree message, still have information in the body. All Lending Tree messages from January (that’s when they started arriving) have empty bodies. All Lending Tree messages from February and later still have the body contents.
For one message, I chose View > Message > All Headers; all header information disappeared. I then chose View > Message > Raw Source; the new window was empty. I was able to copy a message that still displayed body contents back to a folder on the original server. Attempts to copy a message that had the body missing back to the original server failed.
In this case, I don’t really care, but it will make me more cautious about using On My Mac, even on Mojave.