To resolve this specific issue, take the following steps:

1. In GoAnywhere, go to Service Manager and click the cog next to Agents Service
2. Select Edit and click on the SSL node
3. Click on the server certificate and then the export button - this will give you a CRT file
4. Go to Encryption - file Based Keys -  Certificates
5. Select  New - New Key Store
6. Set the Key Store type to JKS and choose a location to save to.  Use the name trustedCertificates.JKS and select a password before saving
7. Once the key store is saved, use the import button to import the certificate you extracted from the agents service.  Provide any name for the alias
8. Copy trustedCertificates.JKS to the agent machine and save in C:\Program Files\Fortra\GoAnywhere Agent\agentdata\keys\x509
9. Update C:\Program Files\Fortra\GoAnywhere Agent\config\agent.xml to reference this new file as follows:

BEFORE:

<ssl sslContextProtocol="TLSv1.2" trustStore="C:\Program Files\Fortra\GoAnywhere Agent\config\trustedCertificates.bcfks" trustStorePassword="*a1:kpVMf2Kz7leXg1xLxCIiUQ==:LncEmXKCqV1988nxIuvhjg==" trustStorePasswordIsEncrypted="true" trustStoreProvider="" trustStoreType="BCFKS"/>

AFTER:

<ssl sslContextProtocol="TLSv1.2" trustStore="C:\Program Files\Fortra\GoAnywhere Agent\config\trustedCertificates.jks" trustStorePassword="PASSWORD" trustStorePasswordIsEncrypted="false" trustStoreProvider="" trustStoreType="JKS"/>

10. Restart the agent service on the agent machine, then retry the upgrade