Did a Alter Online Table, a while later an Assert error occurred and all users were locked out of server, until we restarted service (as instructed in help file).
From what I understand on the Assert.log it was caused by number of fields not matching to what was expected by the application, see below.
Assert.log
Wed Jun 15 15:47:58 2016
==> Assertion failed: ( pstDbfElem->usNumFields == usNumFields ) File: ..\ACE\exprengn.cpp Line: 274
Currently running Advantage Server Version 12.0.0.0