First, reflow does not reset the clock for MSL exposure. The best solution is to run the second side before the exposure time expires. I am curious to know why they must sit for 40 hours.
If that cannot be done, then store the assemblies in a dry cabinet until the second side can be run. This will stop the clock but not reset it.
Least preferred is baking the assemblies prior to the second side run. The default bake temperature is 125C and it wouldn't take that long (bake times increase dramatically with lower bake temps).
Get a copy of IPC/JEDEC STD-033C. This will explain everything.
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