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If this issue is with one key only/one remote only that is not unlocking or locking the vehicle the most common cause for this here is the remote itself needing replaced.I have seen the remote fail in the past before needing replaced for this issue here.Even though it is starting and turning off the vehicle this is a seperate circuit then the unlocking and locking circuit in the remote/fob.
The red light blinking on the remote/fob only indicates the battery(ies) are o.k.
If this is occuring with more then one remote/fob let me know so we can continue.
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Was anything done that may have caused the issue here before the fault occured?
This sounds like both remotes/fobs need resynchronized to correct this here.This is usually done with a dealers SDS machine or a compatible scan tool plugged into your vehicle and can take less then a half hour to do in most cases.If you do not have one of these tools to reprogram them a shop or dealer may have to do this as I do not see a manual way myself for this to be done.
Since this only occured when the battery ran out both times this doesnt sound like a component itself is at fault but more like a fault with programming with them needing synchronized/programmed again.
In some cases holding down the lock and unlock buttons for about 10 seconds next to the vehicle will program them again but usually this will require a dealer or repair center to do this.