This issue only occurs when using the NEW SP UI to Appify a list. After appifying browsing back to the app will reflect that the list is not Appified although it is.
Please note that MS changed the way the New SP UI passes the site URL a week or two ago introducing this issues. We had no warning on this change to be prepared. There are still some known issues when using P&D from a list that is using the New UI and working towards fixes for that. If you need to create or deploy packages please switch to classic view before doing so.

NOTE: Lists that have this issue pre the patch might still have the issue, to fix them Appify the list again but with only DATA / Smartobjects. This will update the category in the db and subsequently you will see you previously deployed artifacts from this point forward.

Applicable to Appit and possibly Blackpearl using O365