Just remember to tell them to re-assign you to a seat (or go online yourself after the credit is applied to check your seat assignment). I learned this the very hard way last February.
Bought tickets sometime in October I think for February 09. in the months leading up to the flight the fare dropped several times (yipee). I called each time to get a credit for the fare reduction on the 5 seats I had previously purchased. Jet Blue was wonderful with putting the credit in my account to use on a future flight - I was in credit heaven.
The day before we were leaving a happily sat down to do my on-line check in and JB prompted me to pick my seats - WHAT?!?!?!?! I picked out my seats when I made my first reservations many, many months ago!! Well, no seats together are left. Wouldn't be so bad if we were all adults, but small children were involved - how am I suppose to not sit with my 4 year old???
I called JB. The rep I spoke to did some checking and figured out what happened and explained that each time you call for a credit, they void the original ticket and repurchase at the lower price - OK I get that. And, unless you have an experiences rep and mention it yourself, they do NOT reassign you to the seats you just voided. This is what happened to us.
Ultimately, the put me and the kids in the bulkhead row. They put DH in the back of the plane and my mom in the middle. Luckily, the morning of the flight, I found two seats together in row #2, right behind me and the kids. I paid the extra $$ and moved DH & my mom together right behind us and all was well.
Just a good lesson learned.