This has been driving me mad too, since in any other app Ctrl+Enter means 'Send'.
Anyway, I found a post about disabling Ctrl+Enter for Outlook with a registry hack; I thought I'd give it a try for Lync, and to my surprise it did work.
So:
- Open Regedit
- Navigate to HKCU\Software\Policies\Microsoft
- Right-click Microsoft and add new key Office
- Right-click 'Office' and add a new key named 15.0 (or whatever your Office version number is)
- Right-click the version number key, add a new key and call it Lync
- Right-click Lync and add the new key DisabledShortcutKeysCheckBoxes
- Right-click the DisabledShortcutKeysCheckBoxes key and select new string value
- Name it CtrlEnter
- Right-click CtrlEnter, select modify and set the value to 13,8 (that's thirteen comma eight)
- Restart Lync (I killed the Lync process and then started it up again)
Now Ctrl+Enter should no longer do anything.
[Update]
If you also want to disable Ctrl+Shift+Enter, which by default starts an audio call, you can add a CtrlShiftEnter string value with data set to 13,12.
To quickly apply both above changes you can create a file with a .reg extension (e.g. FixLync.reg), fill it with the content below and run it.
Note: version number 15.0 corresponds to Office 2013, tune this value if necessary!
Windows Registry Editor Version 5.00
[HKEY_CURRENT_USER\SOFTWARE\Policies\Microsoft\Office\15.0\Lync\DisabledShortcutKeysCheckBoxes]
"CtrlEnter"="13,8"
"CtrlShiftEnter"="13,12"