Hi all,
 
I use Sonar X3e, and I noticed after working on a project for a while it takes way too long to save the file, this is paired with big jump in file size. When I look at the versions ( I save manually), file size, for example, goes to 47Mb from 3Mb. Saving the file takes way too long, and sometimes It kind of gets stuck, and cannot finish saving, at that point I have to rebuild my project from scratch. This is very painful, as I am in the middle of a production. I use auto-save and versioning is enabled, if that is relevant.
Please help, any insights appreciated as to why this happens, how to avoid it. 

Do you mean the entire project folder, or only the {myproject}.cwp file?

CWP file only.
 
I made a new copy of my recent project today, it was 47Mb, now 632Mb! I store wav files outside cwp file in an audio folder.

Melodyne edits are actually saved in the cwp file if left unrendered. It is best practice to use small region FX for Melodyne and render them rather than leave them "active."

I didn't use melodyne for this project. 
In the past I thought it was because of some bad VSTs, but now I only use quality trusted plugins, and mostly Sonar's built-in eq etc. 

Currently saving a cwp takes about 3-4 minutes. It was almost instantaneous this morning when file size was 3Mb. I haven't recorded anything today, just straightforward editing, chopping.
While saving the project, I see a TMP file in project folder, that grows from 0Mb to 632Mb (current size of cwp), that's when saving is done.  There is plenty of space on my harddrive. Harddrive's in good healthy state.
What's happening?

this seems similar http://forum.cakewalk.com/FindPost/2901079

It's often large amounts of AudioSnap info. Saving as a bundle file strips it out - save as bundle, open, re-save using standard procedures.

AudioSnap could be it. I use AudioSnap to chop up drum tracks. But I understand in X3 Audiosnap is neber turned off, but it is a different view, so quite possibly Sonar keeps those zillion info and at some point file gets corrupt. 
 

Anderton
It's often large amounts of AudioSnap info. Saving as a bundle file strips it out - save as bundle, open, re-save using standard procedures.

I just tried to save as a bundle, however "save" button in save as dialog is grayed out. Any ideas why that is happening? Thanks a lot. 

Recovered! Thanks a lot. "Save" buttin was grayed out in Save as Bundle dialog because there were still audiosnap and slipstretched audio in the project. Edit-Select-All Audiosnap/Slipstretched command came handy. 
Thanks a lot for your help. 
 
BUT this is HUGE bug. This is my 4th or 5th incident. And I lost a whole day of work today. Sonar should address this immediately. Even by looking at how audiosnap transient markers are displayed and rendered when scrolling, one can tell it is not a solid implementation.
 
Sonar is getting away from me, getting unnecessarily complex even when I don't want it. Moving from v6-8 to X series was like moving to completely new platform. At the next big release, I'll consider other DAWs as a destination for moving, if it is going to be a complete new experience.
 
Sonar, please learn something from Adobe, their workflow, menus, every major feature are still the same way after so many releases, they maintained operability while staying current.