Dear Studio54,
You are correct in your statement that the R3000 has a hot swappable battery. Even if the replacement battery you inserted into the R3000 were bad it would/should not cause the UPS to drop the load. I have personally hot replaced the battery module hundreds of times in the lab. The fact it did drop the load tells me that this UPS probably has some other underlying problem. Without detailed logs I would only be speculating as to what that might be. The only thing that might have caused the UPS to drop the load, short of a true utility failure at the time you were replacing the battery, would be a faulty electronics module. You may want to replace the electronics module (also hot swappable). I noticed you are in the UK. This tells me that you likely have a high voltage model R3000. If so, the spare part number for the RoHS compliant high voltage electronics module is 407406-001.
If you had HP Power Manager (HPPM) installed you would be able to review your data and event logs to determine a possible cause. If you don't have HPPM I highly recommend you install it. This software is what tells your servers to gracefully shut down after a loss of utility power, it also logs data and event data to help you resolve potential problems, and finally it's free.
HPPM on HP.COM:
http://h18004.www1.hp.com/products/servers/proliantstorage/power-protection/software/power-manager/index.html
