Probe Orientation When Programming CAD With A Flip

Do an assembly. 1 CAD in each orientation.

I create "flips" in almost any program I write. I'm not a fan of having multiple programs for each operation so I have one program per part number and just add "flips" inside that one program for each operation and have individual marked sets.
When I "flip", I reset everything. Reset the alignment to Startup, set your workplace correctly. Put the program in Manual mode. Recall my optionprobe settings, movespeeds, and other settings. Recall my tip and angle (even if it's the same as the flip before). I'll then either import another CAD and offset 12in or more in X (to keep the program separate) or transform my current CAD with the "keep original" option checked. Then start writing a program like I normally would. If the program uses the same exact starting but flipped 180deg, then I copy and paste with pattern from the first "flip" by whatever offset my 2nd CAD was transformed to. But the key is to reset everything so you're basically starting as a fresh new program. One program I forgot to reset my alignment to "startup" and had issues until I fixed it.
Going this route, you shouldn't have issues with probe orientations.

Dy doing an " assembly " with 2 CADs ( 1 in each orientation you need ) and then do what the post above says, you effectivly have 2 programs in 1. This is how I handle all parts that need 2 operations.

I tried doing an assembly with 2 CADs as described, and it seems to work correctly for the 2nd half. Everything in the first half is now working off of the 2nd CAD model, so it's completely out of whack. How can I set the 1st half of the program to not be affected by the 2nd (transformed) CAD?