I have a tornado shelter that I have wired for both 120V AC and 12V DC. All of the lighting is via 12V DC while the AC is used for recharging the batteries and running a 1500 VA UPS system that will power a small TV and radio. The UPS system normally uses two 12V SLA batteries in series. To increase the run time of the UPS I want to use auto batteries instead of the SLA batteries. In order to cut down on the cost of batteries I want to use only two auto batteries instead of three. One 100AH battery used for the main lighting and a 50AH battery in series with the 100AH battery to provide the 24 volts for the UPS system. The UPS system will only use the two batteries when the AC is out which is normally rare. Do you see any problems with this setup providing I install a diode in the UPS battery feed to prevent the UPS from recharging the batteries and use separate smart chargers constantly connected and recharging (as long as AC is available) each individual battery? I feel I have overlooked something but I can't seem to put my finger on it.
What you are proposing would not usually be deemed "good practice" BUT sounds reasonably workable in your case. Two batteries in series with different loads on each will often lead to mismatches in aging and charging. Different capacities = worse again. But in your application this seems "reasonably well catered for".
The two mains based chargers need to have isolated outputs - ie not share a ground (or any other) connection between their output and input circuits. This would usually be what you'd expect. Chargers with a ground input lead MAY have noise filter capacitors from both inputs to AC ground and MAY connect this to DC negative out - but usually not. A simple ohmmeter check will allow isolation to be checked.
The diode in the UPS lead will probably not cause a problem. A Schottky diode will give less loss. A P Channel MOSFET with low Rdson and appropriate connection* will allow a low loss diode to be formed. [Drain to B+, Source to output, gate to ground as long as Vgs max >> 12V).
If thelights never discharge the battery to more than say 90% of full charge then an automotive battery may last a long time. If discharge is often much lower than that then a deep cycle battery may be wise. Even deep cycle batteries should not be taken below say 60% SOC (higher better, much higher much better) for longish life.
As Tim says - try to ensure that the chargers treat the batteries well.
Worst case capacity can be much reduced but this is unlikely.
Mor likely is lack of a properly applied topping / boost charge after use and so a reduction in capacity with time, but usually not a vast one.
A VERY OCCASIONAL deep discharge test - maybe annually - will give you a reasonable indication of batter health. Serious requirements end up with SOC monitoring and acid checking and .... but that is probably beyond what you need here.