Yes, I did click Yes to this dialog box, But I have
no rules that would delete mail from that box.
A rule doesn't have to target a mailbox specifically in order for a message within the mailbox to be processed as stated by the rule when you apply them. If you have no rules that state a message should be deleted no matter what, then no messages should have been deleted as a result of applying the rules, indeed.
Or are you saying that doing that would
only allow mail that meets that rule
No, I'm just suggesting that the mail in your
Sent mailbox was processed by
all the rules, including those meant for incoming mail only, and this may have caused unpredictable results.
By the way there are no other rulles set to delete
email. Basically my rules move files from the inbox
to designed folders based on the sender...
If you have no rules that state that a message should be deleted no matter what, then I wouldn't expect any of those messages to be deleted. I would expect them to be scattered amongst other mailboxes, though... Unless you have a rule that moves messages to a mailbox that, for some reason, doesn't exist anymore. I don't know what would happen in that case...
except for this one rule that also moves sent
email to a specific address to the folder also.
Note that this rule wouldn't even have a chance to be evaluated if another rule moved the message out of the mailbox first.
I'm starting to feel that I just hit a bug and I did
not protect myself well enough, and I've lost data
that I will be feeling for some time.
Maybe. Without being in front of your machine it's difficult for me to know what happened. I'm just throwing out ideas here. I must say I'd be surprised if that was the case, though.