Question about modify the tracks.

Yes, you can add an erase move at the beginning of a track - the first two lines in your example would do that, with Theta changing from 0 to 200*Pi (100 rotations) and Rho changing from 0 to 1 (center to outer edge). Not sure if an empty line is handled "gracefully," and that may be the cause of your reported problem (try removing it). But the example you give, while it shouldn't cause problems (without the empty line), will first erase from center to outside (100 revs along the way), and then circle in the opposite direction about 180 times, staying at the edge (this is the move between point 628.319 1 and point -498.821 1). If you want to force a 100-rev erase before a track that starts at Theta = -498.821, either add or subtract 628.319 to or from -498.821 to get the starting Theta of the erase move (depending on which way, CW or CCW , you want it to erase).

Try adding the single line 129.498 0 at the beginning of your track that started at -498.821 1 and make sure there are no empty lines.

The clicking you hear when the problem occurred is from the Rho axis running into the physical limit of its reach. This causes no problem for the motors or the mechanics, but is annoying.

Thank you, Bruce, I will try those out. 

Look at the reverse HEP.thr  file I posted in the "can we get default tracks".   I did an erase like you want before I ran the rest of the code - and you can see how it makes a smooth transition with no "jump".