Is this happening to for certain items or all items? This is due to a change with your shipping parameters...either item weight exceeds courier limit, etc.
Are you offering real time rates or flat rate for some or all methods? Look forward to your response.
I'm having a similar problem.
I use two Dropshippers, one is Printful and other is Printfy.
Products from Printful are cause the error. When get to checkout and it tries to calculate my shipping it says it gives me an error "that my cart has been updated and items you added can't be shipped to your address." Printify products go through fine.
How are you accounting for multi drop-ship scenario - Do you need to set origin zip on the item for each dropshipper in order to provide an accurate shipping rate to your customer? There is a very simple solution.