You could implement a register which changes its value after each line of program
Example:
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1. Motion 1
2. R[99] = 1
3. Motion 2
4. R[99] = 2
5. Wait DI[1]
6. R[99] = 3
Link R[99] to an GO and you know where the program is.
When restarting the program you could use the register and a jump-structure to continu at the same line of program.