So far so good.
Backupped everything to HD Images on WinUAE
Copied that to my new Microdrive (just 3 partitons, all under the 4GB mark because I did all this with the Install 3.1 disk).
Worked fine, put the MD in the A4000: nothing, not even in HDToolBox, so there might be a problem with the CF reader in slave.
No problem, just hook up the MD as only drive in master. Doesn't boot.
So I made a new Install 3.1 disk, booted it and it does find the MD, but the config is wrong, it's set to: UAE-IDE amiga.hdf 0.3
So click on DEFINE NEW and READ CONFIGURATION, here's where the confusion starts:
UNIT IS NOT A DISK (TYPE 7)!
Cylinders: 15501
Heads: 16
Blocks per track: 63
Blocks per cylinder: 1008
Park head: 15501
Size: -576608K (-563 Meg)
Supports reselection is on
I did something wrong, this is not supposed to be an HDF file, because it isn't, it was selected as harddrive, not harddrive image file. I did a format and then just:
copy dh0: mdh0: all clone
Was this wrong? Or well, what did I do wrong and why doesn't read config work?
edit: I found out I've done all this not on IDE0 but on UAE as hdd controller, might be wrong, so I seleted IDE0 for now.
This is a screenshot from WinUAE:

Now I'm kind of stuck
I'm happy I first made the hardfiles, because I won't have to hook up my IDE drive again for copying, so emtying the MD is no problem for now.
Maybe this is because it's an 8GB drive and WB 3.1 doesn't understand this? I'll keep on trying

Another edit:
Booting from the emergency OS 3.9 disk did the trick for now, now just find out how to get the data back on this drive
