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Just out of curiosity, have you been using the 'propagate forward' feature ('q' by default) on functions?

What you're describing sounds like an issue that arises when variables are given types with bare structs rather than a NamedTypeReference, and using the bare struct means that the type in the variable won't be updated when the version in the types list is. (Digging into this would require some interaction with the Python console, it's visually hard to distinguish from screenshots alone, but 'reapplying' the type like you've described would be forcing it back to a NamedTypeReference making all the update propagation stuff work again)

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