As with anything, backup your modded files, just in case, SkyrimVR - Copy.exe will do just fine;
also, make sure you have ran Skyrim WITH SKSE VR at least once, it needs to create a few registry entries so Vortex and other tools can work properly

It's as simple as renaming

SkyrimVR.exe >> Skyrim.exe
Loader_SKSEVR.exe >> SkyrimVR.exe

remember to spell properly or steam will detect the EXE is missing and re update, promptly deleting SKSE

Now you need to redirect SKSE to your renamed Skyrim executable;
navigate to SkyrimVR/Data/SKSE and open SKSE.ini
you may or may not have one, if you don't that means nothing required it (I.E. no mod requires it, no configuration was saved, etc) you can simply create one


on the very bottom of the file type of the loader EXE for the SKSE

[Loader]
RuntimeName=Skyrim.exe

remember, proper naming :)

No shortcuts, not banner.png, you're done
you can now load SKSE from Steam interface, Overlay and even VR Dashboard by simply clicking on the Elder Scrolls: Skyrim VR and steam will think the popup CMD window is all part of the game, it will still counts you playtime and in-game status like it's the most normal thing in the world,

happy modding

this method only works if you're using Vortex, which trick the game into thinking the mods are in the actual game folder

on the other hand, if you use MO2, it will install the mods on itself and temporarily move the mods to the game when you launch it, and remove once you close it

for a much simpler guide on how to do the same, please refer to
https://gtm.you1.cn/sharedfiles/filedetails/?id=2817400703