Have kept flour in freezer all the time - last time we got out the 5 lb bag it had chunks of flour in it. Can only assume it is caused by moisture in the flour since it was kept in original bag - have never placed the flour in air tight container and never had this problem. Can running the flour thru a food processor to break it up "hurt" the flour?
Not that I can imagine. Many of the recipes I use call for making doughs in a food processor and the first step is often "sifting" the flour by pulsing it a couple of times either alone or with the leavening agents.
This shouldn't hurt your flour, particularly if your recipe calls for sifting your flour.
I do recommend that you consider measuring your flour by weight (if you are able), if the chunks are too big to give you a good volumetric measurement before processing, especially if you're making a recipe that's generally "picky" about flour amounts or specifically calls for "pre-sifted" volume measurements. Processing the flour will likely aerate it somewhat and may throw your volumetric measurements off slightly. Weight measurements shouldn't be effected by this.
If the chunks are small (1/2 inch/1 cm), you may be able to get a good volume measurement before you process the flour.
Consider coming back and letting us know how it goes!