If the BOFD processed the check as paper and it was subsequently truncated then reconverted to an IRD, the BOFD endorsement would appear on the IRD image of the back of the check - just the same as if it were still paper.
If for some reason the BOFD either takes the IRD for deposit or takes a check, images it, and reconverts it to an IRD before sending it for forward collection, Reg. CC Appendix D(3) requires the bank to put its endorsement on the back of the substitute check the same as if it were the original.
Thus, unless I'm missing something (certainly possible, especially this afternoon!), it seems to me the BOFD will always be identified by the endorsement on the back of the check, whether it's an original or an IRD.
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