Scheduling agreement condition type default deletion indicator in backend system

Dear team,
our business process is that-
In SRM system scheduling agreement is created. once its approved from SRM in Backend ECC R3 system the same is getting replicated.
But in few of the cases its been obserbved that the condition pricing is flowing but with deletion indicator selected by default.
I have checked the IDOC for the same but there is no value found flowing from SRM to ECC.
Even searched for the same Material & same vendor in some cases only observed with deletion indicator.
For entire scheduling agreement the deletion conditions are updating that is for all line item in scheduling agreement.
There is no info record exists.
Appreciate if anyone can throw some light over this.

Appa K wrote:
Even searched for the same Material & same vendor in some cases only observed with deletion indicator.
What is the special cases ?
I hope you are using time dependent condition for you SA document type.
Check is it fetching from last PO or SA ?
What is happening, when you are trying to create SA manually via ME31L for the same material and vendor?

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