If you flash a ftf file. They are originally signed by sony. They can flash any time you want.
Flashing ftf, will give you nearly factory state, if you flash data partitin too.
If you are talking about ota uptades.
Mostly rooting will not stop you to upgrade. Unless you did not change any thing in system partition. Like installing deodexed versions, audio packs, mods etc.
Ota updates checks system partition integrity, if origin file infos are not same in ota uptade check list, update will fail. Because ota update could not found files to update. "Basicly"
Just root your phone. Do not mess with your system partition.
When ever you get ota update notification, use ota surviveal settings in supersu or superuser application. Most of time they survive after update.
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