Where's my horsee with the disposable diaper when I need it?
It Depends...
A recharge voltage that can properly recharge the AGM batteries will not be high enough for the flooded batteries. So in recharging the AGM batteries will hog most of the charging as they have lower internal resistance.
If your time off-grid is limited to 1-2 weeks the batteries can suffer through it. Try and separate the two types when recharging. 14.4 volts for the AGM and 14.8 volts for the flooded batteries. Just realize that twi weeks is the absolute limit each time you do this and I would't do it more than a couple times a year at that duration.
I would recharge each type of battery immediately upon returning home. Depending on aging chemistry the batteries will get-along when paralleled from OK to poorly.
Take a chart along that explains proper run and charge voltage for each type of battery.
The 3-cell batteries can be measured individually whilr at rest. If you come across one that is .2 lower than other(s) then this is serious enough to need immediate corrective action. The 6-cell batteries cannot be checked while connected and at rest.
You have a lot of batteries to recharge I would start off with the flooded batteries first because they would encounter sulfation on a two week trip with deep discharges.
Separating the two types for recharging then reconnecting for use is the biggest headache. The age of the batteries - both types, was taken into consideration.