Sounds like you'll have to get it hooked up to a PWIS or PST2 Tester (dealer or independent) and readout/reset any alarm codes.
If they disconnected the battery prior to installing the top, this could cause a 'supply voltage' fault in any or all of the control modules. This could cause the beeps you're hearing.
You might try using a simple OBDII reader, but I'm not sure these will give you alarm codes.
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