You should submit a ticket.
When accounts are linked, there is a primary and a sub-account. It sounds as if your Xbox account was the primary one. I've never come across this, so this may be way off (maybe someone else can confirm or deny this), but it sounds like when you deleted the game on your main account (Xbox), it also deleted your saved content on the server. Since your PS5 is your sub-account, the content reverted to that version.
Linking accounts doesn't merge them. The primary account version of the game is the one that is played on linked accounts. When the accounts are unlinked, there are two separate versions (save points) of the game. If you no longer have the game on your primary account, the servers will look at your sub-account version (for the console you are playing on) when loading.
Again, I'm not saying this is what happened, but by submitting a ticket, you'll know for sure.
Here is an example. I have three consoles. The Switch, PS5, and XBox X. I have three versions of the game, one for each console (XBox X is on Gamepass). My PS5 account is my primary. When I play on my XBox X or Switch, I see the same game as on my PS5. I use my XBox X about 90% of the time and my PS5 and Switch about 5% each. Even though I play mostly on my XBX, the servers save all my content under my PS5 version. If I delete my game from the Switch or XBX, nothing will change on my PS5, but if I remove the game from my PS5, I will have two separate versions (save points) of the game, one for my XBX and one for my Switch. If I make either of those accounts my primary, then I will see the same game on either of those consoles.