Couple of different options, each with various potential issues. (Note, you could still have problems with things like the migrations table and the content type table.)
-
Delete all migrations and redo
makemigrations -
Edit the individual migration files to refer to the proper predecessor
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(Safest route) Drop your database and rebuild from scratch
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Recover your deleted app along with the migrations, delete the models in the app, do another
makemigrations, then squash the migrations - hopefully that might remove all the intermediate steps.
Also see: Removing app in django 1.11, which references this blog post: Cleanly removing a Django app (with models)