rename it, or if that's not possible create a new folder. Then open the Sorting Office and modify the Known filter to move messages to the new folder.
If you create a new folder, close theBat and then move MESSAGES.* files from $KNOWN$ to the new physical folder. Then you can delete the KNOWN folder - both from theBat and the physical one.

if theBat can't find the mail folder, it will exit with an error. Mail folder should be at a place that's always accessible.

The issue with synchronizing several installations has been discussed many times here. The most obvious solution is to switch fr om POP3 to IMAP, where messages are kept on the mail server. This way no matter from which PC you connect, you see always the same, IMAP is in many ways similar to using a web-based mail.
If you don't want to use IMAP there are solutions too. If you use theBat only from one PC for long periods of time (like normally only from your desktop, and when you travel - only from a laptop), then it can be synced by simply moving the mail folder between PC's.
In my case, several installations use POP3 at the same time, so I created a home made semi-imap scheme to keep them synced - briefly explained here
http://www.ritlabs.com/en/forum/read.php?FID=4&TID=6792
It has 2 disadvantages - syncs only messages but not other stuff (filters, address books etc., these I sync manually from time to time), and messages replied on other machines do not appear as replied on yours (replies are available and you can still open them with CTRL+BACKSPACE, but replied flag/icon is not there).

it's not risky (well, you know, editing the registry...be careful..), and a one line .reg file is enough for that.
Actually you'll need 2 .reg files, one for setting the path to network and one for setting it to a local folder. Or make a vbs script that checks if the network folder is available and automatically sets the pat in the registry according to the result.

But the above is not a syncronization.
If you work with the network folder, then switch to local, then after some time back to network, you'll not see messages & changes from the period you used the local folder.
That's easy to handle for incoming messages, you may set 'Leave on server' to a bigger number of days and retrieve them from both machines/folder locations. But your replies can't be synced that easy.