Hi,
In order to give you the most applicable solution could you clarify whether you are fixing your Chain (created from the imported sequence) or your NmrChain (created as you made your assignments)?
Have a look at https://forum.ccpn.ac.uk/t/chain-starting-number-once-the-chain-is-already-created/1277 there are methods for both the Chain and NmrChain objects that should allow you to fix the residue numbering in a few lines in the python console (space, space to open) or as a macro. Then it sounds as if once fixed, you could then delete your existing (gappy) Chain A and change your correct Chain B to be called Chain A and all should be well.
Make sure you have saved and archived first though!
Good luck
Brian