I know how very important for you to use the custom template, Jeremy_T.
Our engineers are still working together for the permanent fix of this issue. If you already contacted our phone support, you'll receive an email notification about the updates or resolution for this one.
If not yet, please give them a short call. You can reach them in QuickBooks Online by clicking the Help menu. Then, choose Contact us and follow onscreen instructions.
In the meantime, you can open the estimate and mark it as Closed instead of converting it to an Invoice. You can also create the invoice and manually enter the info from the estimate.
I'll also keep an eye on this and will get back to you if there's an update.
