Hi Richard,
as far as I can see from the coding (Program RPRAPAFO_ALV form line 514 onwards):
- infotype 0009 does not overwrite payment methods.
- PRAA adds the payment method from IT0009 to the allowed payment methods on the template vendor.
- If the employee vendor already exists, so it's just an update, it adds IT0009 payment methods to the existing payment methods in the vendor.
This is in line with what I seem to remember from the last project, where we had cheque payment alongside bank transfer (but it's a long time ago, so I rather checked the code than trust my memory ;-) ).
It also seems some defaults from FI config come into play, but I'm not too familiar with that.
Not sure, whether the above explains your issue, as it's not entirely clear to me what happened in what sequence in your system, but I hope this helps to shed some light on it.
kind regards
Sven