I never heard of Yellow exclamation marks on EHD's unless there is a driver issue with the USB bus itself or for whatever reason an EXTERNAL HD needs a special driver.
Check the Properties, Windows gives a vague clue, what's up with the device anyway.
You may also check the cables, If this is a USB 3.0 device in a USB 2.0 port you lose performance anyway. - May also the cause for these yellow things.
Use CHKDSK to see if there is any damage on the filesystem level, if PSO2 files are damaged, they will be restored anyway.
Why the launcher isn't running is easily explained, it seem to have "destroyed" itself by revoking your NTFS ACL access rights (the main reason why people use the Tweaker).
I bet someone wrote a script to recover from that temporarily, this phenomenon was the reason for the bad PSO2NA start.
Reinstall the game (MS Version) using the Tweaker (these 77GB will take a while), so you can at least login before your transition to Steam.
Let Tweaker download that. There is a guide how to use the Tweaker, READ these carefully. Both of them. The "Install MSStore Guide" and the "Convert MSStore to Steam" guide. The data trash in the Windows Store Cache will be deleted to reclaim this lost 77GB (or more).
If you still want to change your install type, after your got your "PSO2NA MS" running:
Once you are back online, get your visiphone stuff, logout and do a "MS store -> Steam conversion"
This may take a while, but shouldn't redownload 77GB again. I hope you have a Steam account.
If this went well, you can do the Support code/Linking swap and go online using your Steam.
I don't recommend the EGS, it gave me a headache and wasted 2 hours of my life to get that running before I noticed the Tweaker can do that, anyway.
hope this helps
Edit: Install PSO2 to a custom location. f.e "C:\PSO2NA" or "D:\Games\PSO2NA"...