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Looks like your real issue was having too many apps installed (and then linked them) when doing the update. Also other Link2SD users have run into trouble with a similar setup, while "standard" users (without Link2SD) could perform the upgrade without any problem (just run the su package after upgrading and you are done).
While it is a good thing, that you found a solution, it should also be stated, that the upgrade normally does not cause problems, but users of Link2SD should be aware of possible issues coming up, when doing the upgrade.
My guess would be, that it is easier to de-link and uninstall a number of apps temporarily and then do the upgrade.
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