@laurence5905 I understand your frustration with Apple's decision to lock you into their own repairs rather than being able to do that repair yourself and the fact that it had unanticipated consequences for you.
Yes, the warning is permanent and cannot be eliminated unless you do one of two things.
First, if you still have your old battery, the BMS, or Battery Management System, the little circuit board that's attached to the battery, could be cut off and welded onto a new battery cell. That would give you the benefits of a brand new battery without the warning. However, the BMS would still contain all the old battery data and would be incorrectly reporting the cycle count and battery health to the phone unless you use a device programmer like the Qian Li iCopy device to zero out those counters.
The second option is to use Apple's self-repair program to replace the battery. To do that you have to buy the battery from Apple AND rent their equipment to do the job. That will get rid of the warning as well.
One of the best features of iFixit over other repair sites is that users can make changes to any page, so it's entirely within your ability to go in and edit that page to add a warning to others that the replacement will also give them a permanent notification badge on the Settings icon if you so desire.