The architect has no reason to withhold the payment if the Owner is aware of the situation.
4.2.5 Based on the Architect’s evaluations of the Contractor’s Applications for Payment, the architect will review and certify the amounts due to the Contractor and will issue Certificates for Payment in such amounts. This is to protect the Owner from any liability but in the case that the owner is aware the Architect has to issue the payment certificate, If the Architect refuses the Owner is able to Issue the payment and the Architect is to reflect the payment in the next Payment Certificate.
The Architect will issue a bond of surety for the Contractor and Owner to document the change of Material performance and that all parties are aware of the change.
9.8.5 The Certificate of Substantial Completion shall be submitted to the Owner and contractor for their written acceptance of responsibilities assigned to them in such a Certificate. Upon such acceptance and consent of surety, if any, the Owner shall make payment of retainage applying to such Work or designated portion thereof.
Hey Ibuku, yes the last part you mention is very important. The certificate of substantial completion is a must!