OK, I managed to get rid of the error message. There seems to be an additional hardware fault, causing the reset line of the flash chip to be "not exactly high". Added an additional pull-up an now I can write the flash, verify is also ok.
But I would still like to know what the correct procedure is to read/write the full flash? I had a deeper look into the 16M file I read from the device. It is actually 16 times the same data of 1M. So I am not reading the full flash. Is that not possible? Why is the flash file of the dg4000 than that big? What else is in there and where does it goes? Any insight in the data/instrument would help.