So I have the digital download of Apex Legends. They came out with a Special edition that I want to buy. If I put in that new Physical version of the Apex Legends disc, will I lose my data? Because I really want to keep all my data because I have a bunch of legendary skins and stuff I don't want to loose. I just want to add onto my account what the special edition gives.
The answer is without a doubt no.
In the Physical version, with the goodies that you want is probably a code to get the in-game goodies you will get.
Apply that code to your account and they will be given to your account.
The only way it would replace your current progress is if you parse that code in a new account or they force that code to be used on a blank account, and both are far from probable.
Especially because this is a F2P game, I would guess they don't expect somebody to simply pick up that game from the shelf like 'Huh, looks interesting, I'll see what that is after I put 20$ on it.' They probably expect that those that buy the physical version are already active players.