In Apple Mail messages that I attempted to delete were not removed from the inbox. Instead they turned gray. Same with messages marked as Spam, just grayed out.
I thought this was surely a data corruption of some sort and tried the usual maintenance tricks:
+ Reboot
+ Repair permissions
+ rebuilt Mail index (Mailbox > Rebuilt)
+ vacuumed the SQLite database in Terminal:
/usr/bin/sqlite3 ~/Library/Mail/Envelope\ Index vacuum
Still no joy.
Turns out this is a "feature not a bug".
There is actually a way to turn this behavior on and off:
Mail: View > Show Deleted Messages
It is toggled by Command + L
I think that I must have tripped over the Command + L keystroke at some point and inadvertently activated this feature. I am sure I will not be alone in being puzzled by the result!
It does appear that this feature was in 10.4 I just never noticed before...
