A Web-based computer system is provided with software for processing of inbound messages originating from a back office system. The computer system or web-based application may be operated to maintain the consistency of the information on both systems. A method of operating the computer system and application is also provided. The method, system and application accommodate use of multiple inbound queue server processes, multiple ports for sending messages from the back office system and multi-threaded processing in the web-based application system. The various inbound messages received by the web-based application system are processed in proper time sequence. Every document created by the back office system is identified with a unique primary key. The primary key identifies the type of document and the document number corresponding to the particular document. The document and a timestamp identifying the date and time of the document's creations are stored in the back office database. The web-based application system receives an inbound message including the document information from the back office system. Upon receipt, the web based application system searches a database listing primary key information of earlier received messages and compares the primary key information of the inbound message. If the primary key of the inbound message matches a stored primary key entry, the timestamps of the two messages are compared. The message having the later timestamp is identified as the most current version and is recorded in the web-based application database.