When opening some mods in MWEE, mostly just to see what the mod changes, I get this warning:

"Warning: The number of records was mis-reported in the file header. This might have been caused by the file being edited in a hex or other low level editor. The problem has been corrected and will probably have no negative effect."

Is this bad and should I re-save the mod in MWEE since it states the "problem has been corrected" or can I use the mod as is?

It's usually nothing to be alarmed about. It just means that the info in the header doesn't match the actual number of records. It probably means that someone cleaned the mod with MWEdit or TESAME or something. I avoid saving an esp in EE unless I changed it in EE...it's best probably to open it and save it in the CS.