I'm linking to THIS post where for the first time I've heard of someone suffering from the same problem as me.
Basically, the "This VI claims to be part of a library, but the library is being stupid about it" (I may have paraphrased) is solved by selecting the offending VI intruder and selecting "Disconnect from Library".
Problem: If you're programming in LVOOP and are trying to put together a library, this can lead to not only disconnecting from the library but also all of the VIs from their respective classes. This is a major problem because it breaks a whole load of code and takes literally AGES to fix depending on the extent of LVOOP in the project.
I know Classes are Libraries on the inside but PLEASE give us the ability to view and control membership in a more intuitive way and most importantly independently from each other.
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