KSP Recall is a bag of tricks and stunts to overcome KSP blunders, screw ups and borks - trying hard to do not introduce new blunders, screw ups and borks in the process...
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News from the Front
I finally understood the problem on SubAssemblies (if it will solve Merging Crafts is currently Work In Progress) - I was chasing my tail on this one, the solution I was pursuing was impossible (because the problem was completely unrelated to the way I was trying it!!).
I'm currently testing the SubAssembly solution to see if I didn't created any undesired collateral effect, then I will check merging crafts to see if I got lucky and they were the same problem.