I bought my first two Encores a couple weeks ago. One is a Pro Hunter FX and is non-convertible. The second is a standard Pro Hunter. Is it realistic to be able to maintain zero while switching barrels? Are there any upgrades that are recommended?

Change the hinge pin on the pro hunter. It will provide better accuracy. This hinge pin will not move around. Also a good trigger job.
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https://eabco.com/EncorePin.html

Good luck
Steve

The hinge pin that came with it is pretty loose. Thanks for the tip.

I put one of the 51lb hammer springs in. It actually crisped the trigger and made it as light as I want it.

https://www.bellmtcs.com/tc-encore-prohunter-g2-heavy-duty-hammer-spring-1-hdhs-1

I haven't experienced the need for upgrades on my Encores since 1 to 2 moa accuracy has been ok for my hunting use. The muzzle loader barrel, a 22 wmr barrel and my 6.5x55 barrel will do better than that without any modifications.
The scoped barrels hold zero very well when I switch them on the frame from season to season.

Changing the hinge pin is a money maker for the maker of the hinge pin.. if you are not shooting 1000 yds it couldent possibly make a difference.. if your pin is loose enough to make a difference at normal ranges then it got that way by someone doing bad things to your encore.. a factory pin is very tight and I have never felt the need to change it ,. but if you want to change it go for it...I don't really care....