You can have two separate interim archive set that only include objects currently exist in the environment to avoid any warnings during migration.
However it is just a warning since some objects has been deleted from the source db and no longer exist there. It is really up to you.
This is what normally is recommended and customer experience:
1. Create an interim archive set from source (you can either included the objects no longer exist), but the archive set will contain warnings or just add objects that currently exist.
2. Create an interim archive set from the target db (only include objects that you wish to be deleted from the target, but no longer exists in source)
3. Migrate interim #1 for the changes to go over the target
4. Migrate interim #2 for the objects to be deleted in the target database.