Clip lengths and selections changed by themselves.

Earlier today, I had my project down to precise timing, with movie clips timed to a song. Everything was perfect. I took a break, did not close anything, then when I came back to work on it again, I replayed the video to refresh myself on how everything was turning out, and it seemed like the lengths of the clips changed. The timing was off now, and some of the clips that I selected from a longer movie had changed from one specific segment to a different one, maybe a few seconds ahead of what I had originally selected. What might have happened? Nothing was going on with my computer while I took a break, and nothing about the clips had changed. The timing was just completely different from the time I left the project to the time I came back from it. Again, I left the program open the whole time.

The only thing I did before continuing my editing was to "move rejected clips to trash". The rejected clips were nowhere near the time signatures of the clips I selected to use in my project. I am completely perplexed, and since iMovie does not have a manual "save" option. How do I know this wont happen again? Could it just have been something related to the fact that I deleted the rejected clips that were part of the full length movie that i'm taking clips from? I had each clip down to the .01 of a second, timed precisely to the music. I don't want to keep having to re-edit the clips over and over. Any help or insight would be great.