Sometimes, for some unknown reason, an issue is confined to one specific project and does not occur in other projects. The fact that your troublesome clip worked correctly in a new project would indicate that the problem was indeed project related. I suspect that it will not recur.
Regarding your observation on a different matter that deleting preferences wiped out your project, that cannot happen from deleting preferences. Something else must have been the cause. Deleting preferences does not cause loss of data. It simply restores the iMovie app to the original default settings. Nothing is done to the data or project. The data and projects reside in the iMovie library that is separate from the app. You can delete the entire iMovie app and your projects will still be intact in the iMovie library. When you redownload the iMovie app, you then can access the projects as before.
When one deletes preferences iMovie opens in a new blank library with no projects in it. To find the projects, you need to reopen iMovie in the library in which the projects were created, and they will be there. Perhaps the project that you believe was deleted is actually resting in a different library. Check to see if that might be the case.
If for some other reason you do lose a project, you may be able to find it in a previous automatic backup of your library in the iMovie Backups folder. To get to the iMovie Backups folder, follow this file path from the Finder menu:
Go/Home/Library/Containers/com.apple.iMovieApp/Data/Library/Caches/iMovieBackups
When you get there you will see a list of previous backups of your iMovie libraries Click on one dated just before your issue occurred. iMovie will open in that library. Navigate to your projects browser (where your projects are displayed as icons) and see if your projects are intact.
Since because of your previous bad experience you are worrying that deleting preferences might cause you to lose your project, you can always create a new iMovie library and copy your project to it before deleting preferences. Open both the old and new libraries and go to your projects browser (where your projects are displayed as icons). Move your cursor over the project icon to reveal a circle with dots in it to the right of the project's title. Click on the circle to reveal a drop down menu that will contain and option to copy the project to the new library.
Projects cannot exist independently of an iMovie library. They must reside in the library. If you select the library's icon and do an Edit/Copy and then Edit/Paste it in a new location you will have made a backup of all of your projects. Or you can create a new library and copy your project to it as described above.
Finally, you can keep a Time Machine backup that will allow you to restore an iMovie library to an earlier point in time to enable one to recover a corrupted or deleted project.
-- Rich