Back into business
As stated earlier I decided to redo my SD card using Mr. Fusion 2.2.
As I also use the "Switch to USB" function I have almost everything on the USB HDD: cores, roms, configs ... On the SD card I have Linux, MISTer, Menu and not much else.
After the install I "Switched to USB", installed my scripts to keep my HDD spinning, removed the noexec usbmount option in order to be able to run scripts from the HDD, setup my networking back to fixed IP.
At this point F9 was working and my "Spinner" script running.
Now, time to update. I started just by the normal update script which updated Linux, MISTer, Menu, C64 and a few arcades.
As Linux had been updated I had to redo my settings for the "Spinner" script, the usbmount options and the fixed IP.
At this stage my MISTer was still behaving properly.
Next I ran the update all script which did not update much as I had everything updated on my USB drive 2 days ago.
MISTer is still behaving properly.
So something was broken on my SD card and it was only in the last few days. I discovered it yesterday when F9 was not working any longer, trying to investigate I also discovered that my "spinner" script was not running which also explained why, in the last few days, WinSCP had sometimes trouble to connect with a waiting screen popping up but the connection always succeeded (after the HDD was spinning).
I never had an SD card corruption before and this problem is very strange as MISTer was basically functioning properly.
Trying to think was could have happened a light bulb suddenly lit: SAM!
In the last few days I installed SAM A.K.A MiSTer Super Attract Mode, after install I tried to run it but nothing happened. So I wonder if something happened in the shadows and broke something. May be SAM hates Switched to USB.
SAM will stay in its repository and I hope that my MISTer will have a happy life thereafter.