I currently have one Shopify B2C store and use Xero for my accounting. The Xero app works really well.
I have a second and still developing second Shopify store, B2B as a wholesale branch of the same business.
I want to be able to integrate both of my Shopify stores into the one Xero account (as it is the same business), which at the moment the Shopify made Xero app cannot do.
I have set up all of the backend in Xero to have a separate accounts in the Chart of Accounts and a separate bank payment account to link to Xero so there is no duplication. Essentially the only thing they have in common is the Xero app.
I have spoken to Shopify who said that it is possible, the process is essentially disconnecting one Shopify store from the Xero App and connecting the other store, doing an export and then connecting back to the original store and continuing the process.
Looks like I will be doing this on a weekly basis, but still, I think that it is a bit silly.
Also - I somewhat feel that I would not be the only online merchant to use Shopify and Xero and have two stores.
I am just thinking it out loud - not sure if this would work for you, but here are a couple of thoughts on this. Since this is the same business, you could create different collections in Shopify - one for retail and one for the wholesale - and feed all sales into the same accounting (Xero) file? Creating two accounting files would not make sense since you would need to consolidate financials later and that would be a headache. Inventory syncing would also be problematic if some skus are sold both - individually and as a wholesale. If you use only one app for each - Shopify, inventory tracking, and accounting (Xero), it might help you in a long run. If your wholesale business is a completely different entity, then, you should be creating a different Xero file and connecting a different Shopify store to it will not be a problem as well.