Upgrading R/3 with smallest possible data loss

Currently we run BW3.5; Our OLTP R/3 system is getting upgraded to ecc6 from SAP4.6c. The R/3 downtime for upgrade does not give us time to make entries in LBWQ zero. Is it possible to upgrade R/3 without making queue entries 0 and without suffering data loss for extraction to BW? If there is any alternative to maintain data quality please let me know.

If the structure of the data sources is modified during the upgrade, data loss will occur. Many customers are faced with the problem you are describing. A possible solution could be to schedule as many delta loads as possible during the uptime phases of the upgrade. As such, only the last deltas need to be copied over before the downtime may begin.