They won't reflash it if there are no updates to your PCM (in other words, they won't go in looking for a custom tune, and "fix" it), but if there is an update for your particular VIN, and they do re-flash it, yes, your custom tune settings will be lost. Most programmers will save your settings, so if your PCM does get re-flashed, it's as simple as plugging back in and re-programming.