I have noticed that some of my apps are not updated. I have several apps installed as a flatpak on my Kubuntu 21.10 system. I observed that webchord and callibre are not updated. The falthubpage does mention a newer version for both apps but i get no updates. Even if i run “flatpak update” from the commandline it says that there i “nothing to do” Other apps like Zoom for example are updated and match the version displayed on the flathubpage.
Are you sure that the not updated version you launch is a flatpak app? Launch the application and verify with flatpak ps. Paste here also flatpak info com.calibre_ebook.calibre.