Quartz flute not working (V 1.2.2)

After catching rayquaza and exiting jade tower, my pokemon, which was not fainted and was following me up till then, suddenly disappeared. This has also lead to my quartz flute not working, as I cannot seem to tesseract, heart swap, hyperspace hole etc, and is currently impeding my progress in the game. When I select the tesseract option,the sound effect of celebi appearing can be heard, but since there is no pokemon sprite for it to replace, nothing happens on screen. I tried refreshing the map by pressing P but it did not work.

Edit: Happened to my 2nd save file too,was able to recreate the situation by boxing the follower(it took multiple tries by moving around the mons in party and the pc). It could be fixed by putting the boxed pokemon back into the first slot of party for my second save file, but this method did not work on my first. Hoping it will be solved soon

Edit2: Turns out it was just my armoured ttar not having an overworld sprite, but that is only for my second save file

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