No worries.
Without having to track what is deleted in the SWGAide view this is expected when the "delete after copy" is not selected -- I don't know if people are interested in tracking that, it will make the DAT file slowly grow beyond sense and it would slow down startup somewhat, and also scanning for new mails for those that have thousands of mails. I am not a friend of that option.
What could be done is yet another option that takes effect only if "delete after copy" is selected: something like "delete completely" which deletes not only within SWGAide but also at SWG/profiles/... when a user deletes mails from the Trash folder. Of course it would be possible to make that to rather move mails to a backup folder within SWGAide/mails and people have to empty that one manually, whenever.
The bigger question is always, how much power should SWGAide have, and I am quite conservative and pro-safety, but that also makes things more cumbersome. I mean, if a player considers SWGAide his only interface to game-mail outside of the game he really wants SWGAide to delete when he selects to delete. But a player that just occasionally uses SWGAide would be angry if it suddenly deleted stuff he didn't intend to, right? That is why I try to add safety-belts in forms of backup files and folders.
Either way, I will indeed review this issue once I get the time, right now I am walking over some low-level communication stuff. When SWGCraft was off-line a few weeks ago (just for some hours mind you

) some errors surfaced that the code could handle better. I am also correcting so that harvesters do not continue to "work" in SWGAide when they are estimated to idle in-game. People have also asked for this and that in the past so I guess I should do another review of the "suggestions" thread. And it is summer too
Zimoon