if you have problem in operating ur German bank account from here ,it should be fine to transfer...
just make sure you transfer while you are still in Germany to ur nri account...
get a statement showing the debit in ur German account and corresponding credit in your Indian nri account...
write an loe mentioning both accounts and that u transfered the amount to ur Indian account as you were leaving the country....
it is not a big deal....
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if you have no problem in maintenaning ur account as such you may keep it there also...but what u thought of doing is simple and alright ....
they just want to know the funds are urs and u haven't borrowed....