I get more and more admiration for the root-method.....
So, I formatted the SD card and the internal reader-memory;
then I did a factory reset, and started playing with the device - but the root was still active (me
happy 
)
Why happy?: my reader app is repaired (no stupid errors anymore), and my other apps are all still available (even my custom installed apps)
=> after 2 cold boots, everything still going smooth!

(only the contacts-app is always gone on each cold boot, installing again takes about 5 seconds - but that's the only thing that maybe can change in the future -- if I find lots of time somewhere, I maybe can build a new Android app myself, but..... that will have to wait))
Complete time used for formatting the memory and doing a factory reset: <5 minutes
(and my Adobe DRM is still active on the device)
Just for your information