Yes; it is possible to integrate multiple R/3 systems with single APO. You need to define multiple business system groups in APO and assign to different R/3 logical systems to be integrated(transaction /SAPAPO/C1 and /SAPAPO/C2). Also you can use CIF enhancements APOCF001 on APO inbound to attach (suffix) a unique R/3 identifier along with product and location codes. For this, you have to maintain a Z table containing the required suffixes. You may further refer to application help in the enhancement transaction.
Apart from basis settings suggested, make sure that you are sending exclusive data from different ERP systems to SCM system. Else in CIF it will give error that this master data belongs to different BSG and can not be transfered.
By exclusive data I mean, if some master data say product or location or resource has name ABC in one ERP system and it is transfered to APO system. Then with the same name same kind of master data can not be transfered from another ERP system.
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