This is an issue exclusive to Windows 10 2004.
Did not find much on this topic besides a reddit post that was hard to find. So posting here to give a heads up. Hopefully will get fixed soon.
-latest updates to topic-*
*Related known issue; due to the blank icon if you update chipset drivers, monitor drivers or graphics card drivers this will cause your windows icon cache to refresh causing windows to no longer detect the installation of pso2.
*(TLDR-Some of these are advanced troubleshooting techniques and I do not recommend you attempt them unless you know what you are doing, but as stated here they will not resolve the issue at present time.) Troubleshooting i have attempted to resolve the issue includes; Clean Install of Windows 10 2004, DISM scan/restorehealth, SFC scan, Windows Store Apps TroubleShooter, wsreset, repair or reset under setting>apps>PSO2, uninstalling and reinstalling PSO2 multiple times, changing icon of the .exe file using a 3rd party resource tool, going into Regedit to point to the icon path file directly, clearing windows icon cache and rebuilding it.
*An official response after 31 days has been made. As of 7/15/2020 PSO2 Dev Team is currently investigating the issue.
*STEAM WORK AROUND. For some that can do so, those experiencing this issue with Windows Store Version of PSO2 you can use the newly released Steam version of PSO2. The icon will once again appear on Window 10 2004 Taskbar, etc. while launching and playing the game through Steam. Keep in mind this is not a solution for the Windows Store install so take it with a grain of salt.
I will continue to keep this updated until a solution has been made.