So I did some testing today with these craft on the Mun, and what triggers the error is switching the link mode to docked. As soon as that happens, you can no longer transfer resources within the target craft through the substack that the JS-1 is on. Something about the way the mod changes crossfeed rules upon docking so that crossfeed across the link between the RTS-1 and JS-1 works seems to be the issue. The effect doesn't happen on both craft, just the one with the JS-1. It doesn't happen across the craft with the JS-1: it happens only between the substack with the JS-1 node and the rest of the craft. Within the substack, crossfeed rules still work.
I uninstalled "Kerbal Improved Save System" and "Kerbal Joint Reinforcement Continued" and that had no effect on the issue. To further test, I removed all my mods other than KIS, KAS, "TriggerAu Flags", and their dependencies, which all have parts on my test craft. The error still occurred so it's not about interaction between my mods. Given that I haven't had this issue on any craft w/o Making History parts and it's not a mod interaction problem, my strong suspicion is that there's some kind of subtle compatibility issue with Making History parts and the "docking" mode between the RTS-1 and JS-1 link.
I've tried a couple workarounds. The bug does not appear to occur when the JS-1 link is on the central stack of a target craft. Other tests, like disabling crossfeed on the decoupler before linking the craft and enabling it after they are "docked" or removing symmetry on the decoupler before linking the craft don't have any effect. The tradeoff is that whatever part has the JS-1 on it, even if it's the central stack, seems to have some issues. I can't directly transfer fuel from the refueling base to the central stack when docked unless I turn off "resource transfer obeys crossfeed rules". This is largely irrelevant though: I'm never launching a craft linked by a JS-1 and I can always use the Resource Transfer GUI on the RTS-1 to transfer resources between the craft after undocking them.
For now, I'm going to stick my JS-1 links on the central stack of the craft and that will work (at least temporarily), so no rush on this at all. With my craft files shared, this should be easy to replicate but let me know if there are issues on your end.