Unless some portion of the PSU sensing and control system is grounded on the output side, generally there is no issue reversing the polarity. Only folks who would know are the folks that engineered and configured the cap charger. Some times that is mentioned in the manual, some times it is not.
I like dedicated cap chargers as opposed to HV psus. Cap Chargers generally have a circuit that allows faster, more optimal, charging with far less wasted energy by changing the switching frequency in the PSU as the cap charges.
I would switch to series injection triggering if I were you. External field triggering is so out of date. Some times it is needed because of lamp cooling issues etc. Series injection allows two series lamps to run off a given cap bank, as well.
Without pictures and seeing the system, its difficult to comment outside of generalities.
Steve
Qui habet Christos, habet Vitam!
I should have rented the space under my name for advertising.
When I still could have...