I felt inspired.... until my struggle with bugs made me want to throw my computer out the window -- writing this post instead.
I'm editing an audio track, cutting out parts, and sliding the left and right parts together to remove the hole. Of course, I fuse the two clips together seamlessly by fading them into each other (by dragging to top corner of the clips). This is tedious work. About a dozen times, after I had done this with about a dozen clips, the fade-ins/outs got corrupted somehow, and the clips no longer flowed seamlessly. Lost a few hours of work. This happens repeatedly. I feel like Sisyphus.  Looking for some other outlet for creativity that won't raise my blood pressure.
 
I'm using the most recent version of Sonar Professional.

Do you have Ctl S as a reflex move?   Autosave set decently?   I feel your frustration.  Keep at it though.

+1 to ctrl+s as a reflex move. 
 
Also, use your undo function when something like this happens.  I was working on something similar yesterday and had a project halting weirdness go on when I moved a group of tracks to try to get it in the right spot for the crossfade.  A very weird thing happened to the audio later in the track that blew my whole project.  I used the undo list to isolate exactly which step caused the problem.  I never figured out exactly why it was doing the weird thing, but I used an alternate method to accomplish my task which did not cause the error.  Took a few minutes and some head scratching, but it wasn't very long before I found a suitable workaround.
 
Wishing you luck figuring out your problem.  Stay patient.  Save often.  Things can usually be worked out.  Lots of help to be had in this forum if you ask good questions and come into it with good intentions.

To the OP please take a break from your work and come back to it later. We all get frustrated sometimes and it doesn't do anything good to our BP. The posts above are telling me they are in your conner and understand. 

Ive not experienced this issue myself, but perhaps turning on auto crossfade may alleviate some of the tedium? Also perhaps auto saving with versioning or prodigious use of ctrl s can save you time in the long run if something like this happpens again.

There are still days when I get frustrated! But keeping with Sonar for a decade has definitely paid dividends.

sethmopod
Stay patient.  Save often.

No matter what program I'm using, every five or ten minutes I "Save As" the document under "name - 1",
"name - 2", etc. until I'm done.  Then, if I'm feeling courageous, I'll delete all the previous versions.  Autosave and auto versioning are also active.
 
I've lost my share of work and still get caught once in a while.  The upside is that the work is usually done better the second time around.

mleghorn
I felt inspired.... until my struggle with bugs made me want to throw my computer out the window -- writing this post instead.
I'm editing an audio track, cutting out parts, and sliding the left and right parts together to remove the hole. Of course, I fuse the two clips together seamlessly by fading them into each other (by dragging to top corner of the clips). This is tedious work. About a dozen times, after I had done this with about a dozen clips, the fade-ins/outs got corrupted somehow, and the clips no longer flowed seamlessly. Lost a few hours of work. This happens repeatedly. I feel like Sisyphus.  Looking for some other outlet for creativity that won't raise my blood pressure.
 

 
You have to be careful which clips are actually selected/highlighted.
This happens to me all the time: Putting fade-ins/fade-outs on a clip not realizing that other clips in the same track are selected. The fade-ins get applied to all the selected clips, botching my previous work. Of course, I don't see this happening because I am zoomed into the area of interest.
 
I named one of the control bar buttons to "None" which is set to "unselect all". I use it frequently when editing to make sure that only the clip I want selected is actually selected.
 
Somehow, while moving around the project while editing, other clips get unknowingly selected. Then when you go to edit one clip, you unknowingly edit several clips at the same time. 
 
Perhaps you are experiencing this same phenomenon?

Then there is rewinding the tape for the last listen of the night, on the 2" machine with incredibly lousy brakes, that the studio couldn't really afford to keep in good working order....tape rewinding at super speeds....slowing down by going the opposite direction on the rewind direction...kinda like a boat in water....  HOPING the tape won't snap.....cause you're tired and really don't want the machine in fast speeds anymore.....but....

+1 "unselect all", use key binding.  I use that key as much as any!