Venting -- from a very frustrated user

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.

+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.

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.

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.

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....

mikedocy
 
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. 
 

 
This has happened enough to me that I get really paranoid sometimes. For example, when zoomed in on a very small (apx 2 bar) zone,  somehow I must have selected a bunch of other take clips which were not visible and deleted them.  Saved every 10 minutes or so; problem was, I'd unwittingly saved the mistake. It wasn't until several versions later that I zoomed out  and saw a giant hole in my project. This has happened a few times. Don't know whether it is pilot error or a bug; at all events, the mystery of it all keeps me very wary.
 
Recently I resurrected a project created years ago in Acid Pro 7. It's all audio, and at this point basically just involves shuffling clips around. I decided to do it in Acid rather than porting it over to Sonar. Acid, while quite under-specc'd compared to Platinum, just does these bread and better things so much more easily and smoothly than Sonar, imho. 
 
 
 
 

Deon C recommended auto fade (+1) but you might also consider setting your Cut preferences to Delete Hole. This will save you lots of steps and it might minimize the chance of problems. In fact a single cut command would complete the task of you can live with your presets.

Either way, stay chill. We all learn through our challenges, so you seem to be learning a lot lately.

Just another view...  if you have multiple takes it can sometimes be worthwhile opening Take Lanes just to make sure you're selecting only the desired clips.   If needed you can move the clips vertically so they're in consecutive lanes and add the fades to the "connecting" ends of the clips there.