Whenever you’re testing your game, you’re in client view, meaning testing through your client/player. Clients can’t see anything in ServerScriptService nor ServerStorage since that’s only for the server to see. You can switch to server view to see those instances again
Otherwise if that’s not the case, do you possibly have a script that’s causing everything in ServerScriptService to be cleared?
When testing your playing your in the client mode. Click on the button next to the Stop button that says “Current: Client” to switch to the Server mode.
If the scripts still aren’t there that might just be a normal bug. So I would try just to restart Roblox Studio or create a new place where you copy all the elements from your old game in.
If that doesn’t work try looking for a script in your game that might cause all the elements in the ServerScriptService to disappear.