Remove Workflow from Features I'm trying to remove a Workflow instance from a Feature. But every time I uncheck the workflow and recreate the feature, the workflow gets deleted.

Now I know that with Views, Panels and other entities, all you have to do is to edit it, and it will be shown as overwritten (meaning it is using the database instead of code from the feature), and you can then safely remove it from the feature.

If I edit and save the workflow, it gives me a Revert link in the workflow menu. Yet if I then remove it from the feature, the workflow still gets deleted.

I've tried exporting the workflow and re-import it after removing, but then is just added with a new id (WID), which opens another can of worms on my site.

When I edit and save the workflow, I see in the workflow table in the db that the exportable status change from 2 to 3. I don't know what all the allowable statuses are. But this might be something to look into.
It looks like you've tried alot of possible solutions with mixed success.

A method I'm not certain you've tried is to apply a patch to Features 2.x for Drupal7 that Provides a way to Import Views/true exportables back to the database.

This patch creates a new tab in the Features Admin area called Import if you select the items in the selected Feature to import back to the database, it will then attempt to import the exportable back to the database. Unfortunately as some users note in the thread -- you may not receive a confirmation message that it was successful or not. Recent versions of this patch may have addressed this lack of a status message -- I used this module months ago to move about a dozen features out of Features and back into plain/simple database configuration.

There is also discussion in the thread about Drush Ctools Export Bonus. But I found this module difficult to use and produced an error with (i think) field_group stuff at the time.