I have a similar problem on a Mac mini that I'm rebuilding from scratch (clean install of 10.11.5, followed by install of Server 5.1.5). It previously has 10.11.2 and an earlier version of OSX Server.
Before starting, I made two separate copies of the mini's HD onto two different external drives, using SuperDuper.
Then erased the mini's internal 500 GB drive, installed 10.11.5, followed by OSX Server.
Next step was to run Migration Assistant in order to restore my /Applications folder, and a user home directory.
At first, Migration Assistant found the external drive holding the copy, but it displayed a warning:
"This source is an OSX Server, but your Mac is already an OSX Server. You must first demote your Mac".
It was not possible to select the external drive in Migration Assistant.
A cryptic comment in Charles Edge's TakeControl of OSX Server book suggested to delete from the external drive:
/Applications/Server
/Library/Preferences/com.apple.servermgrd.plist
/Library/Server (folder)
After doing so, the warning about the ext drive being an OSX Server disappeared, and Migration Assistant let me select the drive as the source for the copy. It then display the list of items that can be transferred, and unlike other reports here, I can select/deselect these as desired. But it refuses to actually copy anything: "Not enough space available to transfer".
- The destination drive (the mini's internal hard drive) has 485 GB free.
- The size of /Applications when I select it in Migration Assistant is just over 5GB. There's more than enough space available on the internal drive for the transfer.
- The size of the user folder I want to transfer is 47 GB. There's lot of room for that too.
If I de-select everything in the Migration Assistant list except for Other files & folders (25 KB), it still complains that there's not enough space available to transfer.
Has anyone made headway on this? It appears to be related to the fact that OSX Server was installed on drive previously. What other cruft on the external backup should be deleted to erase all vestiges of Server on it?