Sorry for posting a message on such an old message thread, gents. It's over two and a half years old, so I hope Conny did get an answer
In the maintenance manual, Boeing does warn that leaving the scavenge system operative does run the risk of "in-flight loss of control". There are procedures for deactivating both the electric and hydromechanical pumps in the manual (12-11-5-003-053/-066).
Electric scavenging can be activated at 2 points:
1) when the CWT pumps are on and then go low pressure (not a problem when you leave a large quantity in the CWT for ballast)
2) when the reserve transfer valves open
It's not clear how even aircraft with modifications for carrying ballast can stop scavenging at the second point. For example, Combi ballast modifications appear to consist of only FMC and IDS software/wiring changes, not Fuel System Management changes.
These systems may simply rely on very little fuel being scavenged (in 2 hours) after the reserve transfer valves open.
The hydromechanical system is similar. Fuel transfer should only occur about the time the reserve valves open (but is controlled by float valves in the wing tanks). However, there is no time limit on scavenging with the hydromechanical system.
Rgds
NSEU