My scenario: I have a file with content type "A" and i declare the file as a record. The file is send to the drop off library but the content type A is no longer available. The question here is how to apply content organizer rule without that content type?
When moving a file from a library to another library, in general, we need to keep the two libraries have same content types. Otherwise, the file will use the default content type in the target library(Drop Off library) instead of the correct content type.
For your issue, if the content organizer is based on the content type "A" in Drop Off library, I suggest you also add Content Type "A" into Drop Off library to make sure the rule run well.