Should 1 of the 4 batteries fail by short-circuiting of even just one element (each is made of 3 elements, for 6v output), then the pair of normally working batteries would very quickly discharge through the faulty pair (which would have become a 10v battery instead of 12), overheating both.
May be a rare occurrence, but you can only prevent heat damage by fitting 2 correct size fuses.
I personally believe you can charge them all at once, when the batteries are in good health, with no problems. You may surely separate charge each of the two 12v sets, as well.

For example, DG motorgliders have exactly 4x 6v batteries, each 12v pair being connected to the other and to the main system, including a charging circuit, via a lead string fuse.

aldo cernezzi
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