I am trying to remove my city on beta without scrubbing my whole account as I have another city in syna arda. I don't want to leave an abandoned city lying around. if anyone knows how to do this I would appreciate any help.
I have deleted a city on an account with more than one city by going via Support and they have deleted just the one. Otherwise, as you say, the goodbye tool will delete all cities on an account.Each World server (Beta, EN, US, etc.) is a separate account. If you delete your Beta account your Live accounts are not affected. However, if you delete your Beta account, you can not post on this forum anymore.
To delete your Beta account, use the "goodbye tool". To get there, click the grey Settings wheel in the bottom right corner of your game screen. When the interface pops up, click the little yellow wheel. When the dialogue box opens, click "Data Usage Options", then when the page opens, scroll all the way down to the bottom of the page and click the red button that says "Go To Goodbye Tool". Once there, follow the prompts and do everything the email tells you to do.
Edited for note: On Live servers, if you have more than one city in your account (say you had one in Arendyll in addition to the one in Sinya Arda) and you wanted to get rid of it, you would have to delete your whole account.