RIGHT- I use safe mode often to quicky open other projects for a variety of reasons but yea, DON'T SAVE IT, just close without saving OR save as a barebones version that you can then just open normally
 

mudgel
Just create a copy of the project before you open it in safe mode if you're going to save that file.

I can imagine a situation:
You open a problem project in safe mode > are glad to see it's operable and editable > You go through the track view to check things > " yeeh, everything looks OK,  oh, there's an off time MIDI note, I just nudge it a bit" > "How does it sound without the FX?...Hmmm well, I boost track 3 a little" > you forget you're in Safe Mode and do a reflex Ctrl+S :o/
 

Seeing as others have mentioned not having thought about some of the possible outcomes associated with Safe Mode; I wonder?

If you opened a file using Safe Mode, with Auto Save activated, might auto save be triggered if the set time or operations reach their set limit?

Thanks for posting this.  I came looking for how to load a VST after having opened a project in safe mode and then having saved it.    Good warning that all your effects plugins disappear!   
 
For other searchers:  instead of looking for the words load VST or load VSTi or reload VST or reload VSTi or undo safe mode for VST or any of the other plausible search strings:
 
you go into the browser window, synth section, select one of your VSti's (very difficult to tell it's selected with my colors but the gray changes a tiny bit), then click the little down arrow at the top of the browser window and check 'VST connected'.    Do this one at a time for each one (can't seem to select them as a group, afaik).    Then save the project and you'll be back to a working set of VST instruments.   This does not fix the loss of other plugins, of course, but at least recovers the very time consuming process of reloading a set of instruments. 
 
As to whether it can take a long time to load a project, even with a powerful computer: yes, of course it can.    Loading all those samples can take quite awhile, even with SSDs and fast memory.   Plenty of time to make a cup of coffee, anyway. 

williamcopper
you go into the browser window, synth section, select one of your VSti's (very difficult to tell it's selected with my colors but the gray changes a tiny bit), then click the little down arrow at the top of the browser window and check 'VST connected'.  

It might be faster to float the synth rack or dock it in the multidock. Then each row in the synth rack has a power button. Click the power button to change the synth connected status.

Interesting.   I always have it docked "at the right" and the power buttons are never visible:  so I never even knew there were power buttons!      Thanks.  

does the global fx bypass not re-enable everything in safe mode?

chuckebaby
I always, ALWAYS back up midi when saving projects for the simple fact that if a project goes corrupt, you can always salvage the audio tracks (they are in the work folder) but the Midi is saved with the project.
If something goes array and Project Ducky wont open.. "Poof" there goes the midi !

Maybe that should be a feature request! An option in the global preferences to export/save midi files externally upon saveing a project.
Same as 'copy all audio' -> copy all midi

As long as there are no mix ups regarding newer/older versions. (Especially with versioning option active)