The disappearing Vive controller also happened to me recently (obviously in VR mode). It would work perfectly right up until the main/start screen loaded in VAM. It (controller and laser beam) simply disappeared. The controller also worked flawlessly in every other application I used outside of VAM world. I could not find any help on the internet, and well, I got lazy and used desktop mode for a few weeks downloading and viewing all the while using the mouse and keyboard. VAM worked fine for that.
At this point, I'll let you know I eventually got the controller working in VAM, but I'll also let you know that I do not know for sure what, exactly, the solution was. Exit now if you want to find a quick solution somewhere else. Keep reading if you want my story.
First, I tried the above fix of SteamVR in/out of Beta mode. Neither in nor out mode got the controller working right.
Next, verify the controller bindings were to VAM (must be with VAM running). They were exactly as needed, but the controller still disappeared.
I use "VAMplugins" amazing plugins/addons. One allows changing the laser color. Maybe that was it. Removed/reinstalled each plugin. That did not work.
Checked to see if there was a config parameter in VAM I accidentally checked/unchecked. Nope.
Frustrated, I went to the last backup I made of the VAM folder. It was about 3 weeks earlier and the controller had back worked then. Quick method. There were maybe 5 files in the main VAM folder that had file dates newer than my backup, including the VAMupdater and config files. Hoping for a quick fix, I replaced those files, and the other 3, with files from my backup. No luck.
Long method. So, I renamed the "bad" VAM folder and then restored, from backup, the entire VAM folder from 3 weeks ago. Fired up VAM.exe in the restored folder and YES! The controller worked perfectly. This meant the problem was not with SteamVR or the controller, but it was inside the "bad" VAM folder somewhere. I could have stopped there, but (1) I wanted to provide a solid solution to save someone else hassles, and (2) I wanted to reinstall vars and mods that I installed after the backup was created.
At this point I copied all of the "bad" VAM files, a group of 10 at a time, or folder by folder, into the restored/working VAM folder. But, I made sure to click "no" to ALL overwrites. (Out of 36,000 files, there were about 1,000 new since my last backup.) Then, I would get back into VAM and the controller still worked flawlessly. I did this over and over and over hoping to find "that one file" that was the key. But, there was no ah-ha moment.
In the end, I had the new color laser, and all the new content since my last backup was there. I'm back to 100%. I don't know what happened, exactly, and my best guess is that I had a corrupted "old" file that was not corrupt in the backup. That's it. I know more about what it wasn't, than what it was. Also, I hate when I get the "reinstall" advice, so I won't say it here. Peace.