Is there a safer way to make preprocess changes?
In an ideal world, you would create a sub-theme off of your master theme.  For example, most people don't use the Omega or Zen themes directly; rather they use the starter kit which is included as the basis for the sub-theme.

The sub-theme will inherit features from the base theme, but allow you to customize as needed.  When the base theme gets updated, the sub-theme doesn't get touched.

Whether you can retrofit your theme to actually be a sub-theme depends on your situation, but I suspect it is possible.