It depends on what you were scanning and at what resolution, but in general you're missing out on a small amount of sharpness by scanning them upside down. However, if the scanned images look fine, it probably isn't worth the trouble to scan them again.

The main issue with scanning them upside down (film base down) is that you might put the emulsion layers out of reach of focus for the scanner. The stock trays that come with Epson scanners put the film at the correct distance so that they can be scanned in focus, whether right side up or upside-down. But if you were scanning on third-party trays or thicker mediums like glass plates, you might have issues with the scanner maintaining focus during a scan, as the registration distance for film scanning is within a millimeter range a few millimeters above the scanning bed. It's more likely you would have bad scans caused by film curling in the trays than film orientation.

For the scans done on the flatbed, the same issue exists, but the maximum dpi direct from the flatbed is considerably lower (reputed to be about 600 dpi) than it is for medium scanned in the tray. You'll be less likely to notice a loss of sharpness here. If they're drafts, say, like contact sheets, you probably don't need to rescan these either. In addition, you might run into newton's rings in your scans by scanning directly against the bed.

Anecdotally, myself, I've intentionally flipped some negatives/film when scanning if the emulsion side has a lot of issues (severe scratches, fine embedded dust, rinse marks) or the film doesn't lay flat enough the correct side up in the tray. Some issues are just too difficult to fix and it usually proved faster to just get some reasonable scan done first to get a closer look at the image before committing to fixing the film for a final scan.