1. Always delete pso2_bin manually after uninstalling it from the MS Store.
MUCH LIKE STEAM, the MS Store will NOT delete patched content / user-added content. (The pso2_bin folder is located in the "Program Files\ModifiableWindowsApps" folder.)
2. Always, ALWAYS, install video games on your Operating System's main hard drive.
A lot of older games don't like it when they're on an external hard drive. This is mostly moot on consoles because consoles just read the instructions included in the game's packaged folder. However, on a PC, registry can make or break games, and some software will inherently read a registry value as something hard-coded, such as C:\ being the drive it's installed in despite you installing it on D:\
A great example of this is in MapleStory 2's anti-cheat code, which will shut the game down every 5 minutes if it detects Cheat Engine being installed in the default Program Files directory. However, installing it elsewhere causes the anti-cheat code to not find Cheat Engine, and your game session is safe from harm. (Note: The anti-cheat code only detects if it's installed, NOT RUNNING. This also violates UK/EU laws where software has to tell you that it will be scanning your computer's directories, which it doesn't. IE: it doesn't ask for UAC/admin control.)
3. Make sure the pso2_bin folder has read/write permissions for you.
Because if it doesn't, sometimes programs will just make duplicates in another folder that it can read.
The first two are standard user errors that the publisher/developer can write off. However, the third one is more of an error both parties have to deal with. The installation process itself is what determines the read/write permissions of the folder in question, which is why most installation programs ask for UAC / Admin privileges when you start them up. So that they can actually define these permissions in the first place.
As for this...
thinking this game is a virus
Most antivirus software will think most games, out of the box, on release, are in fact viruses. Because most games are actually keyloggers in disguise. This is mainly so that the developers can get valuable feedback from system dump files/etc. to debug errors without having to ask you for "what you did" every single time. The best way to deal with this, is to tell the antivirus / firewall / whatever company that the program in question is a false positive. People have already done this for the standalone version of PSO2 for Japan, but not for the North American version, which likely uses a new digital signature among other things, which sets it apart from the JP version's EXE file.