There are manufactures that claim their beads are internalized and biodegraded completely. Indeed, we found that cells isolated with iron beads from Miltenyi lost their magneticism after some days in culture (but it could be due to dilution). We didn't see any particular unexplained results with bead-isolated cells.
It's supposed to be possible to remove the beads by cleaving the antibodies with papayin or DTT. We didn't try that. It would allow you to compare head-to-head.