After a bit of research I figured out My ISAM doesn’t support transactions (yes, silly me), so the tests above were done using simple consequent queries (modified up there as well).
However, it seems My SQL does some internal optimizations and runs them very efficiently.
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Visit Stack Exchange This is the usual way how to update properties in EF, and in your case, I'd say it seems the only proper way.
I had a situation like this and using the method above got an order of magnitude performance improvement over the non-SQL way with only ~2000 records.