Unfortunately, you are going to br down for a period of time to accomplish this. Here is my suggestion that would provide for the least impact:
1. Power off the primary and force the stand-by PIX to an active role.
2. Disconnect the failover cable between the 2 PIX's and follow the instructions from http://www.cisco.com/en/US/customer/products/hw/vpndevc/ps2030/products_password_recovery09186a008009478b.shtml#pix_without to recover the password on the primary PIX.
3. Once this is complete, power down the stand-by PIX and bring the primary back on-line. Make sure that the primary PIX (the one with the recovered password) becomes active and starts passing traffic.
4. Re-connect the failover cable and power on the stand-by PIX. During the bootup, the stand-by PIX should sync with the primary and get the new confic changes.
As for known issues, not that I am aware of. Would probably need to see exactly what you changed. Make sure you are always making the changes on the active PIX.
Scott