i have ( had ) the same problem; and here a short description about my WORKAROUND ( and my environment, and workflow ).
my environment:
NFS-Linux share, where my original footage, events and projects are on ( i don't use any local storage )
FCP-X 10.0.1
Motion 5.0.1
everything unchecked on every import so there are just links in Final Cut Events folder
workflow:
FCPX: importing my footage
FCPX: create 1st project
FCPX: place my clips in project-timeline ( more than 100 clips )
FCPX: export 1st project
Motion: post process it and export it afterwards
FCPX: import the post processed clip again ( everything unchecked again, so again just links in Final cut Events folder )
FCPX: create 2nd project, and place the post processed clip there and do lot of other things with it ( e.g. using blade to split it in same pieces so it looks like the 1st project, then color correction, etc. )
each time i export my 1st project, do the post processing in motion, export it, the 2nd porject shows me this "media files changed outside" thing.
WORKAROUND:
just after you export the post processed clip the very first time do the following:
.) open terminal window
.) go to the directory where you placed the post processed and exported clip
.) execute: touch -m -r <exported file name> tempfile ( so the file called "tempfile" gets same access and modification time as your exported clip )
each time you changed your exported clip outside:
.) close FCPX
.) post process your clip outside, export it with same filename as before
.) open terminal window, and change to the directory where this - just exported - clip is
.) execute: touch -m -r tempfile <just exported clip>
.) now the timestamp (access and modification time) is used of the temp file
.) open FCPX
.) re-rendering is needed, but media is connected as expected
even changing the lenght of the exported clip is possible, but then you additionally have to do the following - after you did the steps above:
.) go to the event browser
.) open the clip in the time line
.) drag & drop the same clip ( same file ) from the finder above that clip in the time line
.) after that you should be able to change the lenght of it
.) now the addional seconds are available in the clip in the event browser ( but not in the project/timeline - of course )
so for me it looks like that the timestamp - not sure which one ( access time and/or modification time ) - and the filename is used inside FCPX to reference footage ( events and projects ) and as long as u have those you can reconnect/relink it again, i haven't tested what happens if you remove the file from disk/share and what happens if FCPX is opened before you used the touch command to assign the correct timestamp.
i wish and hope it solves your problem as well as it solved mine.
cheers,
christian