Reading between the lines (and I may be misinterpreting what you wrote), it sounds like you:
Moved into your place in Bangkok, and your landlord filed the required TM30.
You subsequently obtained an extension using an agent. The agent have contacts in Chonburi, so they moved your address to Chonburi to get the extension.
You now try to file a TM47 in Bangkok, which obviously is not going to work, since your official address is in Chonburi.
In order to file the TM47, your landlord need to register, that "you moved back to Bangkok". Your landlord not unreasonably reluctant to do this, as from his point of view, you never moved away.
If I am correct in the above assumptions, then the only way to get your TM47 done, is for you to persuade your landlord to update the TM30 (monetary incentive?). Immigration in Bangkok is correctly refusing to file the TM47, until your address has been updated via a TM30. I am afraid this is just one of the complications with cutting corners and using an agent to get your extension.
Immigration have no problems with you moving between provinces, but it is a legal requirement to file a new TM30 every time you move.