To update an existing certificate, you need to create a new certificate for your Pass Type ID in the Apple Developer portal and upload it on Passcreator.
To do this, first go to the certificate section of Passcreator (https://app.passcreator.com/en/passusercertificate/index).
Copy the Pass Type ID (the name next to the icon in the list of certificates) whose certificate you want to update and click on "Add or update certificate".
Click on "Update an existing certificate" on the next page.
To create a new certificate in the Apple Developer portal, you'll need a certificate signing request (CSR). Download it on the page by clicking on "Download certificate signing request" and log in to the Apple Developer Portal afterwards (https://developer.apple.com/account/). Leave the tab open where you're using Passcreator since you'll need it later again.
After logging in on the Apple Developer Portal, click on "Certificates, Identifiers & Profiles".
Now click on "Identifiers" in the menu on the left and click on "All Types" on the upper right. Click on "Pass Type IDs" to filter for Pass Type IDs. Look for the Pass Type ID whose certificate you want to update. Click on the entry in the list of Pass Type IDs.
Now you'll see existing certificates alongside a button to create a new certificate. Click on "Create Certificate".
The page you see now shows a form asking for the CSR file. Upload the certificate signing request you've downloaded from Passcreator earlier (filename: upload-to-apple.csr) and click "Continue" afterwards.
Apple now creates the new certificate and shows a page where you can download it. Click on the "Download" button to download your certificate.
Go back to the Passcreator certificate section (if you should have closed it in the meantime, this is the link that takes you to the correct page: https://app.passcreator.com/en/passusercertificate/new - click "Update an existing certificate).
Upload the certificate file that you've downloaded in the Apple Developer Portal (filename should be pass.cer) by selecting that file and clicking the "Save" button.
Since you've updated an existing certificate, the system will tell you that you've updated it.
If you want to update existing passes with the new certificate which makes sure that users are still able to open it, edit your template. You don't have to actually change something, just hit save and publish the changes afterwards which makes sure the existing passes are being recreated using the new certificate.