Before you spend time to find the files differences in the site/mods between primary and secondary server, you can use the following steps to bring up the secondary server services.
1)Stop secondary services.
2)Backup nx.env on the secondary.
2a)Change @NX_VER_CTL value from UPGRADE to DISABLE.
3)Start secondary services.
Then, the secondary server should be up and run. Logon web UI should be without problem.
After that you can find the file differences in the site/mods between primary and secondary server, copy the file from the primary to secondary and restarted services with the @NX_VER_CTL=UPGRADE in secondary server nx.env.