Hi Tkoboss,
welcome to the Apple (user-to-user) Community.
Re: My rail pass disappeared in Apple Wallet
You have tried some good trouble-shooting methods aslready:
Some passes (eg considered expired) may be hidden and yet can still be recovered:
(If you don't want to automatically hide your expired passes,
you can turn this feature off in Wallet & Apple Pay settings):
For more info: scroll down to "Expired passes" in Remove passes from Apple Wallet - Apple Support
Else
Maybe check if the pass was added somewhere else in Wallet: eg: as a transit card
Add a transit card to Apple Wallet - Apple Support
or
Use Express Mode with transit cards, passes, and keys in Apple Wallet - Apple Support
or
Add, use, and share boarding passes, tickets, and other passes in Apple Wallet - Apple Support
More info: How to: Keep cards and passes in Wallet on iPhone - Apple Support
More Support if needed:
You might want to reach out to the iPhone Support: Team:
(There's a "Get Support" link at the bottom of their webpage... link below)
iPhone - Official Apple Support
All the best :-)