Thank you for your post!
-Is your Windows Server 2012 R2 machine dedicated to FileMaker Server?
-Do you have any third-party anti-virus or backup software?
-Can you determine if there are any particular schedules or client side activities occuring when the problem starts?
-You might try running Recover on local copies of your files (via FileMaker Pro) to check for damage.
-You can try to stop the FileMaker Server via your Services Tool or via CMD line: net stop "FileMaker Server"
Before resorting to a forced restart of everything, you might try restarting the admin console--which can be done from a command line. You are no worse off if it doesn't work.
review the LOG file - maybe you can determine if there is anything still holding on to it.
also check if schedules are terminated.
i had that case back using FMS13 and a backup kicked in while i stopped the server - so a deadlock situation forced me to force quit ..