I'm not sure WHY this is happening, but I've experienced the same thing.
In my case I worked it out by off-line-ing and then re-linking the clips.
In your Project bin right-click the merged clip and "Make Offline". Obviously choose the option to leave media files alone. Then just right click again and "link media". It should already be in the right folder and if you check "exact name matches only" it should find it right away. I even managed to do this for a bin full of clips.
They need to figure this is happening and fix it-- cause it sure is annoying. But in the meantime hopefully that work-around will work for you as well.
I had this happen to me last week - and while I didn't get a good answer over on the COW forums about whether this is a bug or a feature, there was a workaround - but annoying to lose 4 hours of work first.
I had to make the audio clips into stereo (Clip>Modify>Audio Channels) and then merge them with the video. If I started them as mono files, then it would happen every time. (usually every other track would go to negative infinity audio gain)
Then, when you drop your merged clips into your timeline, they will show up as mono tracks. When you close and reopen, they should remain.
Anyone else have an idea if this is a bug?
Sure seems like a bug.
And for the record when it happened to me I did have 2-channel sound as dual-MONO set in Clip>Modify>Audio Challens (from an external sound recorder) being merged with the video from DSLR footage.
I take it back-- My fix does NOT consistently work. It's happening more and disconnecting-reconnecting media is not fixing it. This is majorly frustrating. I could try what needles27 is saying, but that sets me back to the beginning on this.
This stinks. Anyone else have any ideas?