I am coming across this same issue. Fortunately the project I’m working on i will probably never have to reference again. Here is what i did. Right click on the project you want to consolidate in the project library – Duplicate Project or highlight the project and command D. Pick the 3rd option and it will create a new event with only the clips you used. That was helpful for me because i keep all my light leaks and transitions in other events. So if you have clips from multiple events it will grab all of them and put them all in a new event. The duplicate project will have (fcp1) after its name. I copied the new event folder and new project folder to my backup external. Then from within FCPX delete the events and projects. I opened up the event & project on another computer and it was fine except for a difference in plugins. I reopened it on my computer and it worked fine. This is the way it worked for me, that doesn’t mean i will not be crossing my fingers each time.
let your fingers do the walking