The question is:
Do you consider production buildings as Sugar Mill(large or not), Indigo Plant(large or not), Coffee Roaster and Tobacco facility as empty spaces for the replacement of colonist on the ship?????
Yes, all free spaces are counted, be they on a pink or a production building.
Do I have to keep only 1 of them or Can I keep all of them.
You can keep all. You may keep one barrel of any one good (standard) and you may keep all barrels of any one other good. So you can see it as not keeping the one standard barrel but keeping all barrels of corn.