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I rooted my HTC One X just to get FM and other AT&T blocked apps installed in /system/app directory. Now there is an OTA update and I'm sure it will unroot the phone. My question is will the FM app stay and work after the OTA? Thanks.

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This mostly just depends on how they distribute the OTA. If it formats /system then yes (Kindle Fire does this), if it's an incremental (patch) update then probably not. –  eldarerathis Sep 10 '12 at 18:05

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As eldarerathis already said in his comment, this very much depends on how the OTA is performed. First, some OTAs might even fail to execute, as rooting modified the /system partition and they check the CRC sum which then no longer matches (I had that with my HTC Wildfire/Buzz more than a year ago).

If they don't care about CRC, the answer still is "yes and no": Some OTAs are just "incremental" (replacing/adding single files); those wouldn't touch your root-apps, and root would be retained. However, full updates (and this includes most "version bumps", e.g. from Android 2.2 to 2.3 to 4.0) are completely "replacing" the /system partition; in this case root is gone along with all the other system apps.

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