The safest way is to export the history and then import into a local Galaxy to double check that everything was exported correctly and completely. (Before purging from the source). It is a good idea to back up your data anyway. Whether using Galaxy or not.
There are a few known issues with certain datatsets that do not export as expected. These are composite datatypes and those given the same "name". Trello has details and we are working on this, but I would recommended just checking yourself for completeness. Any data that is not exported as expected in a batch history export can be download as an individual dataset and saved. Or loaded into your local.
If you do use a local, be sure to keep it backed up! Instructions for all admin activities can be reached by starting at http://getgalaxy.org
Hopefully this helps! Our development team will jump in if there is more advice. Jen, Galaxy team