This is a byproduct of the built-in safety feature that prevents you from accidentally overwriting a legacy file with a new version. ID considers older files opened and converted in newer versions to be brand new files, and for new file operations like Save or Save As ID always defaults to the last location where you did the same operation.
Thank you for the answer, but for me it creates hassle in my workflow. I just wanna keep working seamlessly after updates, not have to struggle to resave. Pehaps a choice should be given to the user, or the path remembered but an additional warning dialog given when overwriting a previous version file?