There's a default and per-room retention setting
1:1 chats are not automatically purged.
Note that these retention options differ between HipChat Server and HipChat Cloud (hipchat.com).
Short answer, Nope .
If you will only create a procedure in the application server to swipe older files or a database job then you have nothing to worry about.
Now if you want to customize the hipchat code to have that feature atlassian is pretty open about working on the code of their products (same goes for Confluence, JIRA and the rest of the party):
As long you don't re brand it and re sell everything is fine
The only thing that atlassian will no do is to support customizations, if you change the hipchat code and break something you will not be able to reach their support for help on fixing that (you will need to fix that on your own or reach a atlassian expert).
I can't confirm for sure, but from my experience with the atlassian suit I don't believe deleting those would be harmful.
This kind of data is dynamic and if removing that would cause harm to hipchat I'm pretty sure that atlassian would store it into the database and not in the file system .
A simple test, just for confirmation, would be to set up a test installation, chat a couple lines and then just remove the files.
You could also raise a support ticket and also get confirmation from one of the atlassian hip chat engineers as well:
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