Further to irish's comments..
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Originally Posted by Antiacus
When i complete a mission should i quit the game, reload sh3 commander, then reload the game?
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If you want updated date based files, yes. Otherwise you'll still have files copied in based on your previous patrol start date, and not your current patrol start date. This is covered in the User Guide.
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Originally Posted by Antiacus
If so, is it also true at a resupply ship?
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If you want updated date based files AND you don't want to spend 30 odd days docked, then yes. This is also covered in the User Guide.
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Originally Posted by Antiacus
Lastly, does the patrol sector assignment have anything to do with your starting port?
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At the system level, SH3 will pick a grid based on your flotilla and sub-type when you dock at your home port. Due to the way SH3 indexes certain files though, if you dock at some other port, you will get a NULL grid.
I say at the system level because the appropriateness of grids chosen is based on whatever mod you have installed. If the modder understands the grid selection logic, appropriate grids should be chosen. If the modder doesn't understand the logic and throws random grids wherever, then the appropriateness decreases.
For GWX, Rubini and I spent a bit of time matching appropriate grids to flotillas. What I didn't get around to doing before I left the team though was to review the appropriateness of the grids based on sub-type, although knowing the flotilla.cfg file intimately, I am quite comfortable with its contents. For other mods though, YMMV.