I figured out why I was getting deleted files when I downloaded them through bulletproof ftp. There’s a box in the advanced settings that I swear I have never seen before. “Delete files after successful download”. Maybe it’s just that the config location was moved. I’ve been using bpftp since win95 and have NEVER seen it before.
Now that I have figured that one out I am currently uploading all the files it has deleted 🙂
I have also upgraded to MT 4.0 Beta, so be prepared for the entire site to be hosed for awhile.