You might experiment with using G92 to reset the axis in question. Best stop the axis on a whole number of turns from zero, but not absolutely necessary, I guess. Just that you'll need to break up your toolpath into manageable lengths, so whole turns is convenient for that.
I've done this on my 96 Haas, but I don't think I was going that distance. Strangely enough, after achieving a certain distance, and resetting with G92, and going some more, I did reach a limit where the jog handwheel would not take the axis any further in that direction, but the machine still responded to programmed movement.
You can view the total of all of your G92 commands in the offset register, as each one adds to the one before it. When you get to the end of your program, you can view the register and record the value of that axis. Then you can zero it out right there. But for repetitive programming, you'd probably want to reset that axis at the end of your program, with a G92 value of opposite magnitude to what was recorded in the register. Note that efficient unwinding of a highly wound up axis can also be handled with careful usage of G92 commands. By that, I mean always know where your axis is at (in whole turns) before you alter that axis dimension with a G92 command. Otherwise, you can get seriously lost and really muck up your part.
