I've gone through many VCSA issues in the past and my conclusion at this point based on my own observations and experiences is that the only predictable outcome with messing with VCSA is to scrap it and start from clean install. I've had cases where the integrated VCSA updater would render an appliance useless, not booting or booting but not functioning correctly. Literally a GUI "update" could do that. So in summary yah it is a hassle but the alternative is a support case that may or may not lead anywhere.
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