I figured it out finally. It might be that this is only a problem when you are using RA mod like Im doing.
Anyways, what you need to do is turn of link data. If you do that then you can update all you want. Interestingly I discovered another bug thats also very annoying:
If you towed contacts, link off, and autocrew for TMA station; and then turn the link ON.... You can now say goodbye to some of your towed contacts forever. DOesnt mattter if you drop tracks and re-tag them or turn link off or whatever. Seem to be random which tracks you lose, but they are gone!
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