Good questions, its impossible to say from here if it ever had its polarity changed or not but here are some guidelines to follow:
1) A generator can charge at EITHER battery polarity and once properly polarized and configured correctly it can work fine.
2) NOTE if in doubt one should Polarize BEFORE start up because if the genny were polarized opposite from how the battery is installed the Voltage Regulator might be damaged.
3) TO POLARIZE the Generator once the battery is installed and BEFORE start up, use a jumper wire to momentarily flash jump from BAT on the VR over to the GEN/ARM terminal and you should get a small spark. If its a cutout relay instead of a VR its still the same BAT side over to GEN/ARM side to polarize BEFORE starting...
4) If a working ammeter is installed correct and polarity is matched if you turn lights or ignition (unless a mag) on, it should swing over to - discharge, then when running at fast RPM if alls well it should swing over to + charge. If an ammeter does just the opposite the polarity must have been changed and to make the meter work right swap its leads side to side.
5) If its a battery powered coil distributor ignition polarity does matter. For POS ground the coils - gets voltage when IGN is ON while the + wires to distributor. For NEG ground its the opposite. + from ignition switch and - to distributor.
6) If the genny is working at fast RPM battery voltage should rise from say 6+ or so up to at least 6.5 to 7 volts subject to RPM, battery and genny condition. Twice that on a 12 volt system.
7) As is, does the ammeter show + charge at fast RPM and a small discharge when off and lights or ignition ON ?? If so it must be okay. If it does the opposite, discharge at fast RPM but + charge with lights or ign on not running, the ammeter needs its leads swapped. HOWEVER if batt voltage rises (see above) at fast RPM it must be charging !!!!!!!!
8) To be safe I would polarize,,,,,,,start up,,,,,,,see what ammeter shows running and not running with lights/ignition ON,,,,,,,,,,,,,see if battery voltage rises at fast RPM (if so must be charging).
If 6 volt it was likely POS ground original and Id keep it that way. If so install battery at - ground,,,,,,,Polarize the Genny,,,,,,,,,start her up,,,,,,see if ammeter registers correct and battery voltage rises at fast RPM...
NOTE this is for GENERATOR not an Alternator. Most Alternators are for NEG ground.
NOTE BOTH the Genny and VR need a good ground to work
NOTE you asked if starting on Neg ground automatically re did the Polarity. It may have damaged the VR if genny polarity was opposite from battery installation. Sorry, I cant say from here what happened when you started it (don't know if polarity was right or not???) or how it was wired before or got changed ??? so just Polarize BEFORE starting and see what ammeter does and see if battery voltage rises at fast RPM ??..
Nuff said for now, let us know
Best wishes yall keep safe and God Bless America in these difficult times
John T