Not a lot to go on but here goes. I suspect you already know most of this anyway, but are new to VR.
First things first. To prevent this in the future, once your controllers are properly mapped in VR, open your settings folder, find the proper VR_[controller name].jsm, pull up the Properties dialog and mark the file as read only. Then make a copy of the locked file as a backup. Do the same for your 2D monitor [controller name].jsm version as well because sometimes it’s more convenient not to be using VR.
Assuming you have enough time free of distractions, and the patience, I recommend going offline to make any controller mapping adjustments. You said, “when I put the headset down it will initially let me map the oculus but…”
Yeah, no. That won’t work. Switching back and forth like that appears to leave AH in an unpredictable state. Map your controllers for VR with the headset on, or at least fool AH into thinking it’s on by covering the sensor before you remove it. Map for all 4 modes. Remember that when you select mode 2 through 4, the “Copy Mode 1” button becomes an active time saver. For VR, I recommend setting the Auto Select Mode ON. Otherwise, every time you switch to a GV etc. you’ll be in fighter mode 1. AH does not save your last mode for the next sortie. If this auto mode switch is on and you haven’t mapped all your buttons properly, well that could explain what you describe right there.
Before you exit AH, Ctrl+Alt+Tab out and check that the jsm file has the current date and time. Open it with Notepad and inspect the entries for missing data. If the text reflects the changes you’ve made, close it and follow the read only and backup advice.
You might be tempted to rename a copy of your 2D jsm file to the VR file name. You can’t depend upon this working because the first two lines in the files may not match. It appears AH keeps a hidden record of these first two lines and will overwrite the entire file if they don’t match expected values.
I hope I've anticipated correctly what your issue is and you find this helpful.