How do I edit a project without losing files?

Here is my workflow. I record two live tracks of live instrumentation, up to an hour or so at a time as a sequence of like 5 or 6 sections back to back. I save out the project. Then I go to to isolate one section by editing out previous and following sections. I re-save as a new project. Then I reload the entire project and I get a Missing Files notice where a lot of the original aif's are missing. I can usually recover these from my trash bin, but often one track has been shortened so it no longer fits into it's section with the other instrument.

Any suggestions? Currently, I'm making sure I have a backup of the original before I do any editing, but it shouldn't do this I wouldn't think.

Thanks.