I've been trying to sus this out and I'm not getting very far with it so its time to ask you guys to test this for me if you can to see if its a proper bug or just my brain malfunctioning.

OK I'll go through the steps.
1/ created a pyramid using the EBE.
2/ deleted the EBE file leaving just the .dbo
3/ place the .dbo on a map and was able to see and change the properties tab
4/ saved the map and when it reloaded the model was set up as an EBE e.g the properties tab was missing and the tab to edit it as an EBE was there (obviously you couldn't edit it as the EBE file is gone)
5/ retested sent the model to Graphix who kindly converted it over to a .x (thanks m8)
6/ replaced the .x on the map saved the level = same result
7/ saved the map out with a different name = same result
It doesn't seem to matter how many times I do this every time the map is saved the model be it a .x or .dbo it still appears as an EBE model?
man am I now confused
can anyone test this for me please

If you have now converted it to a .X file are you still using the same .fpe file ?
You may need to remove the command below from it … or make a fresh .fpe file
----------------------------------
;EBE Builder Extras
isebe = 1
----------------------------------

Brilliant thanks synchromesh