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Hi, no disconnecting the alarm siren will not affect the operation of the power door locks.
Are the locks not working since you disconnected the siren?
Has the siren been disconnected yet? Is the fuse still blowing?
They are not being truthful with you. It sounds like they are trying to sell you more work.
You could try turning the wheel all the way to the left to access the back part of the liner and see if you can remove the retainers and peel back the rear section. It will be pretty difficult to do it with the tire on. You only need to jack up the right front but you really should put a jack stand under the car for safety.
It has nothing to do with the siren. Have they replaced the fuse? Do the power locks work from inside the car?
If the locks work from inside the car try pointing the remote directly at the door handle from a few inches away and see if the locks will unlock. New batteries in the remote might help.