The code will run fine as long as the mode defined in the preamble is what the code is written in.
For example say Mach is set as default G90 (Abs distance) and G90.1 (Abs IJ) and your code was written in incremental for both then as long as you code had G91 and G91.1 in the preamble things would run fine. If however your code did not specify which modes to run in then Mach would try and run them in the mode it is presently in.
Hood