@vmarko I installed the patch fix on one of our staging environments and it does seem like the issue has been resolved. No console errors and /wp-json/ was not empty with the linked patch (v2.9.4) installed. Thanks for the quick turnaround!
Also experiencing this issue since plugin updated on 6/17. Current version is 4.1.20. With this issue we now have a permalink url included in the sitemap as well as our custom url being added under the additional pages section so this is time sensitive. The update has wiped out all excluded posts that previously existed and the exclude posts field won’t save anything after refreshing the page.