Is it possible to copy and paste bones from one armature to another in edit mode? Joining the two armatures with Ctrl J is not an option in this case since it breaks a lot of other stuff.
Shift D to duplicate the bones, P to separate them into a new armature and Ctrl J to join to the target armature is the way, so you have to understand what is breaking and why.
The target final armature has to be last selected, so it will retain its name, loc, rot, scale, and so on.
Both armature should start with everything applied (loc, rot and scale, Ctrl A).
All bones should have their own unique name before joining.
If theese conditions are respected, nothing breaks with joining.