Right. In TS2006, the limit is 256 (makes sense, since it's 8 bits).
Now, in TS2009 it appears that either that limit has increased drastically, or is unlimited.
A while ago, I did a test board to have a look at the textures available, and put each and every one on the board.
It was over 400 textures, so either the number has been increased by one bit to 512, or it's a lot higher than that (perhaps 65536, or 16 bits).
You can use a 3rd party app called Erazor, which is a two step process.
First, you paint over the area of the board you want to erase, then you run the Erazor program separately (after opening the route for edit), and it removes all of the ground textures from the painted area.
You will find all the info you need on Erazor here:
http://forums.auran.com/trainz/showthread.php?t=1471
Then, you need to DL the Erazor mesh from DLS:
http://www.auran.com/TRS2004/DLS_viewasset.php?AssetID=82855
Problem here is that you may still have the same unwanted textures elsewhere, and you may not remove as many as you think you are, so may still be close to the limit.
I guess I could just suggest you upgrade to TS2009. In 09 you can replace textures (as well as any other assets). It can take a long time, and mine has crashed a couple of times while trying to replace textures over the entire route.
If you do a section at a time, you're OK.
And if it turns out that you're already running 09, then I'm baffled.
FW