No that's not a bug. The file in question is being automatically generated at specific intervals by some background timer tasks located in oxTrust. It's updated
because the source attribute(s) for the custom nameID need to be updated depending on how they're configured in oxTrust.
If you want to make your changes permanent , you will have to unpack/unzip the oxtrust war files , then unpack/unzip the jar inside named `oxtrust-configuration-xxx.jar`. Inside , you will find the file `META-INF/shibboleth3/idp/saml-nameid.properties.vm` . Do the necessary changes based on the backup file , then repack everything.
Let me know if you need further instructions