Any changes via rj.com will not make a difference at this stage (flight under airport control).
OP, try the app using the ticket number?
Whenever IB has an aircraft change, they e-mail out (perhaps not in your case, due to the codeshare) an e-mail saying you have been reseated. That's probably why your 'old' seats show unoccupied. Though if it's a 345 (i.e. 346 with no Y+) I don't think any seats in J are numbered exactly the same...