correct me if i'm wrong but in the governance tab of company you can actually say who owns what, so I believe as long as it's "personal owned" set it shouldn't be an issue.
Just to add to it, some of the old flags may need replacing after the update, best way to check it is having a friend create new company and run around your land to make sure all flags work correctly. Hope that helps!
For those you don't know, you need to replace you flags with new ones for the 3 day thing to work. I'm just doing that currently with my mates.
EDIT;
Some flags will work right away I recommend having friend to check which claims work correctly (have him start new company) and which don't.
we managed to build one (after around 6+ failed attempts. what we did was;
1) standing on the shipyard (that lower part that connects to sides
2)keep looking into inv when its about to be crafted
We will be attempting to build schooner soon but idea is look in inventory and imagine boat will spawn in front of you.