I'm not sure how I would deal with one of those.  I'm lucky that all my business-use vehicle owners retired before they changed the rules on like-kind exchanges.  And then took away employee business expenses. 

But let's say the car cost $25,000 eight years ago, and the value at trade-in was $12,000.  And for one year, it was driven 10,700 business miles, which I think comes out to about a $3,000 depreciation equivalent, and 50% business use.    If you subtract the $3,000 from the $25,000, you still have a basis of $22,000.  If you subtract the $3,000 just from the $12,500 basis for the business-use half, you still get a basis of $9,500, and that's more than the $6,000 proceeds for the business half.  

Of course, the miles could be a lot higher and the business use percentage could be a lot higher.  Let's say 21,400 miles and 80% business use.  That $6,000 depreciation, subtracted from $20,000 basis for the business part.  Still a loss.  You're not subtracting the whole standard mileage rate amount, are you?  It should be just the depreciation part of it.