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Are there any issues with enabling full encryption and loading custom ROMs or will it be seamless?

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There's some related discussion here: Will a Custom Recovery work with an encrypted device –  eldarerathis Aug 3 '12 at 15:40
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Encryption is done on the /data partition (where all app-data is stored). However, /sdcard is sometimes encrypted too (if the sdcard is actually internal memory of the phone i.e. not removable).

If the sdcard is also encrypted,then you will be unable to flash ROM's from within Recovery (recovery can't read encrypted sdcard).

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Updating is possible with some extra steps: You can circumvent the latter problem by using a tmpfs mount for /sdcard and 'adb push update.zip /sdcard' just seconds before flashing. C.f. this answer –  ce4 Aug 3 '12 at 17:17
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If you have an unencrypted /sdcard(this is usually true if you have removable SD Card slot), you can install zip from sdcard as always.

If your sdcard is encrypted,too, but you have relatively new device and software(Ice Cream Sandwich or newer), you may be able to use sideload.

  • Choose install zip from sideload option in your Recovery

  • Run this command on your computer: adb sideload <filename-of-update.zip>

Then you can continue to flash the ROM. (In my case, the installation process started automatically.)

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