FIXED - NO APP REQUIRED!
I've called Shopify so many times about this and thought I'd try again today. I had a really helpful guy on the phone that explained when you add a second location the system automatically changes from single shipping origin to multi and you can't change this back... BUT SHOPIFY CAN.
If you call and ask them in the back end to change your setting from Multi Shipping to Single Shipping Origin the shipping system doesn't look at the locations you are shipping from but looks at the ADDRESS OF YOUR STORE ACCOUNT. You still have the locations live and stock files for both locations but it just ships from your store address.
They changed it with me on the phone. We then tested 3 orders. All orders worked and didn't reset anything. I was able to order the same things a few times so all good.
There is one little catch... In Single Shipping Origin you cant use the collect from store options. For me who doesn't offer this anyway it's not a problem.
I hope this fixes the issue for you too, although I understand some may be working in other ways.
You know....this actually DID work.
I actually took a screenshot of this response and sent it to shopify support with a link to this forum page and they gave me the instructions to switch to a single shipping origin.
First I had to delete any other shipping profiles I had set up so that all products I have in stock were under "general shipping".
Then the support team did whatever they do to activate the single shipping origin.
I was afraid this might screw up the connection with Printful (a dropshipper that auto-fills per order) but it appears to all still be working and not charging double shipping when customers go to buy from both my warehoused items and Printful items.
It's true that you can't offer a pick-up option with this set-up, but if you don't offer that option, this seems to be the solution.