I've experienced some strange install/maintenance scenarios with z/OSMF, but have managed so far to get it all put back together again. I went from z/OS 1.10 to 1.12 with z/OSMF, which was a bit tricky with all the config file changes, but I haven't had any problems with PTF's. You just need to NOT take the holddata literally. They give you the parameters to run the shell script. but the user controlled variables, like config name and location must be replaced with those required for your environment. The doc in the hold could be worded much better.
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