If the old scope was off that much(~2MOA at 100 yards, WOW !) then yes old inputs on the Sig will be off. Did you upgrade to the Mk5 or warranty it ?
What are the outputs for the new HD-b's ? The old ones gave MOA but it was rounded to .5 , drop in inches, and a couple others but I found that the "clicks" on the scope(.25 MOA) to be the most accurate. For example, if it ranged 500 yards then it would display a "20" which meant 20 clicks on the scope which would be 5 MOA.
Again on the different cards, you could not rename them as different files for identification or it would corrupt the file. Hopefully they changed this as I labelled them in little zip lock bags which really seems stupid for such an "advanced" piece of tech.
Good luck and keep us posted