Revisit assertion vs warning in preprocessing script

[jmelot]

I've moved to assertions in cases where we've discussed the check and should break preprocessing if it fails, but weshould be thoughtful about when we do this, as Neha notes below. I will think about this again later.

Not blocking. The general trend in this file has been to convert printed warnings to assert statements. Should this also become an assert someday?

Originally posted by @niharikasingh in #110 (comment)