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I've got a 99 NB with the older style 1620 button cells and upon replacing them the remote ceased working.

I coincidentally have a bad door lock module on the drivers side (bad microswitch or whatever it is) so no way without the remote to unlock the car and tell it the door was opened ( unless maybe I open the trunk first?).

Car is not starting, alarm goes off when key turned to on position and after enough tries it stopped going off ( hope I didn't disable it completely).

Any help before I pull this lock module would be greatly appreciated.
 

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No start issue: have you checked, the basics: fuel pressure, ignition spark, compression, scan for trouble codes, etc.

As to the remote: basics, are the batteries installed correctly (+/-; in correct position,etc), do they have a charge confirmed with a multimeter, are the battery contacts, have contact, is the red light coming on, when the buttons are depressed, etc.? My Key Fob, will stop working sometimes; say, for example, when I forget it is in my pants pocket and run it through the washer machine. I find, if I disassemble the key fob; down, to the circuit board, spray it with contact cleaner or dunk it into isopropyl alcohol, work the cleaner into the buttons, by manipulating them, to work in the cleaner, bent the contacts to the battery, to confirm the contacts are under contact pressure and replace the battery, it will start working again!

The 99 New Beetles; do not have a immobilizer built into it and so, I don't think, that would be your problem.

The alarm going off randomly; is probably, your door lock module failure and is very common issue. A VW factory level scan tool; like VCDS by Ross Tech or OBDeleven, could read trouble codes and allow, you to view live data, to confirm the microswitches are working.

Got any history of your car; did it ever run correctly, how long have you owned it and are there any variables, like parts that were changed or work done recently, that might be causing a no start issue?
 
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