Originally posted by knighttemplar1960:

My way around this is to dock. Build a work bench, a portal, and a couple of chests. Make sure that you have room and weight in your inventory to hold all the items to make the boat. Make sure auto gather is on. Then stand on the mast and take your axe to the boat until it breaks. As you drop into the water the materials that went into making the boat will go into your inventory. Portal back to your base and put the boat materials away.

Tale the portal back to your ore source/new island and go mine. Fill the chests by the portal with your ore, portal any other goods back to your base, repeat until the ore vein is tapped out or you have enough ore to fill your boat all the way up. When you portal non-ore goods for the last time grab your boat materials and portal back through.

Rebuild your boat at that island and fill it with ore then decide if you are done at that particular location on that island and if you are dismantle the chests, then the portal, then the work bench and sail the ore home. If you decided you aren't done with that island or you want to continue exploring from that point leave the portal and the work bench and after you have unloaded the ore break the boat down again and portal back.

Rebuild the boat at that location, tear down the portal and then the work bench and sail to your next location and repeat from the top.

Always keep a portal open at your home base for exploration (and it doesn't hurt to have an emergency portal set up too.)

Pretty good suggestion, I'll do this from now on thanks!
Other comments though, haven't witnessed it happen just came back to the boat to find it like that. The second time it happened though a friend I was playing with said he saw the boat in a vertical position before it broke. Also hasn't happened in the swamp, every time has been along black forest or meadow shores. Also It's always been stationary when it happens never flipped a boat whilst sailing. I got this game when they first put it on EA and this is the only playthrough I've ever seen this happen.