Base data should not be altered once it's imported, for various reasons - one of them being what you're seeing here: accidentally turning real numbers into Calculated data means that they will get wiped with each calculation.
Sign-flipping can be easily achieved with Aggregation Weight in Relationship Properties, between a given child and a given parent. Set that value to -1 and let the engine do the rest.
If you really want to do it in Rules, you should brush up on the consolidation sequence and understand how you target specific Consolidation members, so that you don't wipe Local values.
