In my tests on Mac, Audacity is actually faster when copying in files before editing.
I did that to a two-hour show editing session once and trust me, it did
not speed up.
Sudden, unexplained computer insanity can be caused by your hard drive filling up. Go > Utilities > Disk Utilities > Select your system drive. Mine is Macintosh HD. At the bottom of the frame, it should tell you the size of the disk and the amount you have used. Edit systems need at least 10% free space to work right. Some people claim more. If you're tight on space, you
really need to fix that before you do anything else. Fuller than the 90% full point, the MacOS may start to act funny.
While you're in there, you can Verify Disk and Repair Permissions if everything else is OK.
Another, pretty serious thing that can cause show insanity is Audacity. Audacity 1.2 is not fully supported on modern Macs. You're fine until Something Happens and then there may be troubles until you upgrade.
The current version for all Macs is Audacity 1.3.12 from here...
http://audacityteam.org/download/
If you use lame to get MP3 or FFMpeg to get other formats, make sure and get both of them from the same place. they're not all the same and you can't use the older versions.
As a compulsive engineer, I'm horrified you overwrite files as you go, but I'm pleased you keep masters and originals isolated and safe. We have posters who insist on editing and overwriting
capture originals and that's just begging for trouble.
You can certainly Save an Audacity Project and that's fine as long as you understand what the rules are. It's not "A File." Audacity saves Projects which are collections of sometimes hundreds of files that make up your show. You can't easily move projects and they're brittle and easily damaged.
Audacity 1.3 will open Audacity 1.2 projects.
Koz