I'm not sure what we're talking about here. an EBB is a system rather than a component, there's the shell as part of the frame, the insert which fits into the shell and there's the BB itself.
If the insert is offset in the shell, just loosen the bolts, take some tension off the chain and push it back, if it doesn't push easily, take the chain and one crank off, remove it, clean and grease and try again (It's a good idea to remove and grease from time to time anyway) If you're having problems getting the insert out of the frame, there's a Thorn video somewhere. Thorn will have chosen the components to give the right chainline with the insert flush. Well, I find it hard to imagine they wouldn't have.
If the BB isn't flush with the insert, that may be normal depending on the type of BB/crank you have. The left side loose cup of a Shimano ST often sticks out a couple of mm.
If you have any issues a photo would help.
Are you sure it hasn't always been like that? Have you re-tensioned the chain? It's quite easy to move the inset to one side when doing so.
I have in the past deliberately run an insert a couple of mm off centre to get a perfect chain line with an older crankset. There's no harm in doing so, there's plenty to clamp onto.