Although a genny can still charge at either Pos or Negative ground once polarized, if battery polarity is changed the ammeter leads need swapped/reversed or else it will register bass ackwards. Also if the battery is at incorrect polarity and you dont correctly re polarize the genny, a Voltage Regulator can go badddddddd.
The typical 3 position light switch is for low charge and high charge usually on 3 brush gennys that use a simple 2 wire cutout relay versus a full fledged voltage regulator.
I think I would re connect the battery at the original correct polarity,,,,, POLARIZE the genny,,,,,,,,, start her n see if she charges or not?????????? If she charges a correct connected ammeter will swing to + charge at RPM,,,,,,,lights will glow noticeably brighter from slow idle to fast RPM,,,,,,,,,and battery voltage will rise from 6.3 volts setting to around 7 at high RPM (twice that on 12 volt system)
If you need my complete long winded Troubleshooting Procedure for NON charging, post back n let me know