I’m sorry for the frustration but that’s exactly how this plugin works. If you delete a hashtag from the text, the tag will be removed. Since it is not possible to differ between manually created tags and automatically generated tags, all tags that do not appear as hashtag in the text are removed from the post. Unfortunately there’s no other possibility, because the main target of this plugin is to be 100% compatible to “normal” WordPress tags.
This behavior is described in the manual https://petersplugins.com/docs/hashtagger/#settings_advanced_nodelete. There is option to turn this off. It’s called “Do not delete unused Tags” and can be found in the “Advances Settings” tab. I thought that should be self-explanatory. If you activate this option, all existing tags are kept in any case. Even if you delete a hashtag from the text.
I have provided this option exactly for this purpose. This option exists since version 3.0, released on 2014-12-21.
Regards,
Peter