Ugh, the old megasync client I always use because its on my external storage didn't want to sign in so I tried a newer one. Big mistake. They broke how the syncing works, it began randomly deleting my files with the intent to delete all of them only to then redownload them again. I stopped it and thankfully got the old client to work again, it had to redownload 300 files back.
Nothing was lost as it at least stayed on the account so it was able to download everything back, and locally it didn't delete anything it just moved it to a recycle bin. So my data wasn't unsafe, but that was not fun.
But, all is good now. I got the old client up and running again and its sync fixed everything.