If you are running vendor-written software in your shop, it is a good idea to check with your vendor before using the Reorganize Physical File Member (RGZPFM) command to reorganize their files. The reason for this is that, to increase processing speed, some vendor packages base their processing on the relative record numbers (RRNs) of the records in their files, instead of on file keys. Attempting to reorganize those files may mess up the RRN processing and make recovery extremely difficult.
So the best thing to do is to check with your vendor before you do any reorganizing. He may have special options or instructions for you to follow. If you take a few minutes to check into this process before reorganizing, it may save you some hassles later on.