There would be no problem, all the vanilla data goes into a new "schema", assuming that is how you set it up, and should not interfere with the other data.
Vanilla uses alot of pre created files to access the database, the vanilla code to access the data would not work, though normal MySQL would.
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Vanilla uses alot of pre created files to access the database, the vanilla code to access the data would not work, though normal MySQL would.