Solving a Smart Mailbox problem - missing messages

We have two work computers, both using Mail, and with all incoming emails accessible on both.

I run a competition which people enter by email, and I set up a Smart Mailbox to store entries. The Smart Mailbox is set up to look for all emails going to competitions@xxxxx.com and with a particular subject line.

All these emails used to come in to our main inbox but they would also build up in the Smart Mailbox. We would delete them from the main inbox but they could still be found in the Smart Mailbox.

Until this week! Suddenly the Smart Mailbox has lost almost all its messages (over 2000 entrants). I think this MAY be because my colleague has been deleting the competition emails from the inbox BUT THEN emptied the trash in Mail (via 'Erase Deleted Items').

So I have two questions:

1 Can I get those emails back into my Smart Mailbox?

2 How can I accomplish this in future? I need to be able to separate out and collect these competition emails (which I thought I had done) BUT we still need to be able to clear out unwanted messages which slow Mail down.