I'll muse on the subject, but this should be taken as musing and not a strict design effort.
If your issues include connecting only at certain times, then your VPN might as well be treated like an FTP-class connection. In a way, this makes it easy to choose a design of sorts. The trick will be to keep everyone using the same versions of everything.
Twelve sites, twelve databases, twelve LOCAL copies of the application. Performance will not be an issue. If they are to stay separate, then let them always and forever be separate. Once per day, start up a procedure via the Windows Task Scheduler on each machine. Read up on Access Help for Command Line Options, specifically /X {macro-name} as a way to run something macro-ish in your databases. (This presumes the machines will be running untended OR that you will have someone leave them on until a time after this process is done.)
So... build a macro to EXPORT via query the files needed for your database update process. In the batch file triggered by Windows Scheduler, run access with the /x to trigger the export to a file. Then use some sort of copy command or an FTP command or SOMETHING to actually transfer the file. If it is a VPN and you have a mapped shared drive, this would be easier but not absolutely required. Just lots easier.
Anyway, this macro runs on each remote machine to take a daily data dump and send it to the central site as a file. Make each file name predictable either by file name, location (sub-folder name) on the central server, or both. Put some import code in your centralized MDB to pick up the files so happily sent to you from the other sites.
Just musing in overview mode, you understand. Run that around a bit and see if it makes sense in your environment. If so, explore the options. If not, it was just a thought that MIGHT have worked.