I had a similar situation for 2 years. Living in Bkk but visa obtained in Phitsanulok.
Eventually I had it corrected at Chaeng Watana. It took some time as they did not like me living in a different place than what was declared on the visa application. But they did not charge me any fee for not reporting my TM30 (Bkk does not care but many other provinces do!). For the switch of 90 days report, they were happy to do it with a copy of my lease.
You should explain your situation to immigration at CW. They will sort it out. But don't stay in Chonburi's books.
It can be an issue if the company terminates your employment and has your WP. If they don't let you know when they cancel it, you can end up in overstay. Normally you have only 24 hours to leave. You can extend by 7 days but you need to know what day it is cancelled.
Try to avoid agent. If you have to pay for your non-B, he will cost you a lot more than doing it yourself. It is not that difficult and you just got the best advice here.
Also if it becomes a bit difficult, a bad agent might just give up or make you pay a lot more.