Just ensure you have done as @AxelVienna writes:

@AxelVienna said in How to save updated subdirs project ?:

Tools->Options->Environment->System->Ask for confirmation before exiting

You should always have that set. Then you don't have to do anything to explicitly save, like anything else you change in Creator it should save automatically or warn you on exit. You should not be experiencing your:

If I just exit the next time I reopen QTCreator my changes are gone.

Do not see any one file marked by X , but I can select it.
However - was was hoping for something like " save whole subdirs as ..."

I don't really understand what you are trying to do :(
A subdir project, does not contain any code, it is only used to define which libraries and executables the project contains and define the dependencies to build them in the right order (cf. https://wiki.qt.io/SUBDIRS_-_handling_dependencies)

So which files do you mean?

Do not see any one file marked by X , but I can select it.

However - was was hoping for something like " save whole subdirs as ..."