Uhh.. yes, you should delete the site, but not before you do certain things (if it's not too late already).
If you have an ITG card.. or several, take screen shots of every config page in the IP Telephony properties pages.
Write down your numbering plan..
Print out your Templates (if you haven't found a way to save them (I haven't)).
When you create the new site, it should be "Site: Name of Location" and "System: Model of your system." This gives more info than the generic "Company name/Company name" that some people use.
Retrieve the System Configuration of the PBX. Fill in the numbering plan manually or you won't be able to create phones.
Then, Retrieve all CPND Name, Retriieve all CPND. (Yes this is different.)
Then I don't remember if you should rebuild the Employee Database from CPND first, or go for Stations next. Do it either way, but I think you should build the Employee DB fist.
YOU NEED THE EMPLOYEE DATABASE!! You can't stay in synch without it.
Retrieve Reserved TN's. This includes the Call Pilot ones, the Attendant Console, voice mail, etc..
Now, make three promises:
1. Never routinely use Reconcile All again. Use it only when you think you have stuff in Optivity that isn't in the switch, and you want the Optivity stuff to go away without affecting the switch in any way.
2. Never create a station until you have created the Employee first. And then "assign the station to an existing entity" Never use "Create new employee" again.
3. Stay in Installation Mode. It gives you time to think before you send changes to the switch.
Optivity was designed as a billing system. The Employee Database can wreak havoc with the CPND in particular. The Employee must exist before the station does. Call it a design quirk, call it a PITA, but do it.
If you have enough TN licenses (to use double), you can just create the new Site in addition to the one you have. Then take your time setting up the new Site based on the info in the old site.
I've skipped a ton of steps. Go to Optivity class at GK. I can't remember them all.
Good luck!