Hi Wreford-Brown,
from my tests it seems that SH3 remembers the waypoints in a save game IF the unit is not rendered when your patrol starts.
Waypoints of rnd layer units are definitely saved (this is confirmed easily with my zigzag rnd layers). As far as I know it's not possible that a rnd unit is spawned in your 'render area'. Therefore the 'scr harbor problem' does not exist for rnd units.
To summarize, as I understand the problem it only exists for scr units in the 30km area around your home port. As Stiebler pointed out, in this case the problem is not very crucial.
Cheers, LGN1
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