The software bleeds the inj pump and fuel filter, which isn't emptied by the injector removal. Air is in the line that goes to the injectors and air in the injectors themselves.
I guess common rail bleeds easier. My tdi with rotary pump was a bitch to bleed after nozzles changed.
I don't see any harm there since the inj pump is not dry. How much cranking did you have to do?
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