That's why they have that transfer of CAR5 form, you send in certified copies of your log book pages or any relevant proof of anything you think you should be entitled to (and the certification can be done by an instructor carrying out a flight review, say, so you don't have to get a JP or whatever), and it gets put on your Part 61 licence.
If they have lost anything, all you have to do is prove you had it originally via log books etc and you'll get it, plus the first Part 61 issue is supposed to be free, so get everything you possibly can included when you first get one issued.
Edit: if there's something you think they missed, there's another form to redress that.