There is a script supplied with P6 that will do the job for a whole directory tree (i.e. a Runtime).

Windows menu, select Python Scripts, click on Utility Funcs.
You should see buttons for "Compress Files" and "UnCompress Files".
When you click on either of them you'll get a dialog asking you to chose a directory, and some other options which you can set.

I suggest you try it out on a copy of a small Runtime (or just unpack a single item to a temporary directory), just to get a feel of what options you want to use before running on an important Runtime.