Jeph:
No, a totally different sound. I have a 2000 (non-S). There are 5 short beeps that are much softer sounding than the warning beeps for the lights on, etc.
Weird!
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.
If you've got an after market radio there is a wire on the left hand side of the radio frame that you need to disconnect. I think it's brown and blue. If you leave it connected and replaced the head unit the car thinks the head unit was stolen.
I saw this tip on this forum and removed mine when installing the Avic D3
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2001 Boxster S
Desnorkled
Pioneer Avic D3
JL Audio 6.5 inch subs (in the door)
Pyramid 4 channel amp