I have a similar issue. I am using a workspace with many projects and packages, and when updating today to xcode 13.2 all the targets to my packages disappeared and now my projects won't build. The error was missingPackageDescriptionModule. Tried recreating the workspace but still when adding packages, local or remote, their targets are not created. Didn't have any problems with the betas of xcode 13.2.

Same issue, started today right after WWDC ended.

I'm not creating it, the schema is already in production. I'm trying to modify a record already being used in production, but the indexes get deleted, so i'm left with a production environment with indexes and a development environment without indexes. When I reset the dev environment, it goes back to the one in the production environment (with indexes) until I make a change, then it deletes the indexes, leaving me again with a production environment with indexes and a development environment without. This causes the app to crash when I run it using the development environement because none of the queries make sense without the indexes. I hope that makes clearer the situation I'm in. In any case thanks for the reply, at this point I'm willing to try anything, there's always the possibility I did something wrong at some point, or forgot to do something at another, or maybe it is something else entirely that I'm missing.