On the RC3R layouts, we frequently have guests bring engines that are run "at home" with a transformer. Running their engine with the DCS is a real treat for them. At the end of their run session we routinely do a factory reset. Then, we unplug the TIU and do a quick conventional run check with the Z4000 just to ensure that there will be no issues when they return home.
I can't think of any negatives associated with a Factory Reset.