Thank you so much @woonsanko and @jasper.floor, issue solved.
We actually do deploy to ROOT, using maven-assembly and the following config:
<file>
<source>site/target/site.war</source>
<outputDirectory>webapps</outputDirectory>
<destName>ROOT.war</destName>
</file>
This has been working in our production site since mid last year, and I know we have created new working document types since, so wasn’t the problem.
This was the answer. When looking at the generated site.war, I saw last modified date was a few months back, even though I have been recompiling often. It turns out none of the modules were compiling.
It seems someone here made a change in the project parent POM at some point, which changed how we should compile ( i.e. should now be in non-standard way), without communicating the change.
Thanks for your insights, they guided me to the solution.