Yes, it will. "flatten true" only flattens cells with a few rectangles in them---it's specifically meant to work around the problem in which Virtuoso likes to make tiny subcells out of everything, including contacts, which makes magic perform poorly (or extract incorrectly, apparently. . .). But it won't flatten everything.

Maybe add an alias of "gds flatten onlysmall" for this so that it's self documenting?

@Riking28: My preference is just to fix whatever is wrong with the code that is causing the substrate not to be connected to the contact in this case, so that it doesn't matter what "flatten" is set to. I just recommended it as a stop-gap measure while I track down the bug.