Quartus optimising out big bunches of logic

Hi there,

In my project, I noticed Quartus is optimising a lot of sub-module components in synthesis. Interesting thing is when I run the sub-module synthesis, its components are in tact.

How can I make sure Quartus maintains hierarchical boundaries? I enabled 'Incremental compile' switch as an experiment. But did not do any improvement. I am using Quartus 23.2

Thanks

Binu