I'm going to guess that someone bypassed or removed the ammeter. Has the ammeter been showing 'discharge' all the time ?
If so, then the ammeter is still wired in.
We don't know if the rerouting of the R6 wire was caused by, or resulted in, damage from the bulkhead alternator connection to the main splice.
If there is no damage I would definately put an R6 wire back the way the factory had it.
If there is damage, then its a little more complicated.