Bone fixing methods

So I just finished up yet another very long troubleshooting problem which went like this:

1.Made some animations with a ported model (CZ terrorist model)
2.Found out that the gun that he is holding looks totally skewed from what it looks like in 3dsmax
3.Spend a while keyframing the bone that the gun is skinned to, with no difference
4.Find out that there is two bones with similar names “Line01” and “line01” Realize that the compiler is removing one of them (find out that its removing the capital one which just so happens to be the one that is skinned to the gun)
5.Compile a few times with “line01” removed, then remember that in order for this to work all ref models AND sequences have to be consistent in that removal of the bone in question
6.Think that this is probably a lot of work and there has to be a better way than exporting everything from MAX again only deleting the other bone each time.
7.Try $renamebone. It does not work
8.Take a risk and open all of my sequences and ref models in notepad++ all at once and replace all instances (with case sensitive ticked) of “line01” to “linex”. Save all files
9.Compile
10.Open in HLMV and it looks just as it should have in MAX

Now what I want to know is if there is any other methods of fixing this, say at the compiler… or another QC command im missing?