SOLVED: (I reply myself)

I ran the one kernel command instead of the dualbooting one and now it is charging.

flasher -F DFL61_HARMATTAN_40.2012.21-3_PR_LEGACY_006-OEM1-958_ARM.bin --flash-only=kernel -f -R

My N9 runs both meego and nitdroid. I hope nothing got mixed up. I stopped the process (control+z) at 1% of battery level, so flasher should not have copied anything to the phone yet.