I just made an upgrade of my development machine to Mac OS X 10.11.2 (from 10.11.1). It is very big download, almost 2 Gigs. I did not uninstall FMS and just left version 184.108.40.2062 on it and ran the OS upgrade without doing anything to FileMaker. All files came up successfully. I have tested WebDirect and it is working and ODBC connections. I have the MBS and Base Elements plugin on the server and calls to those plugins all are working. So far it is looking like a smooth OS update with no glitches.
FYI, the hardware is a Mac Pro (Late 2013) Cylindar with 3.5 GHz 6-Core Xeons, 32 Gigs RAM.