Save As > Created a folder consuming more space

It sounds like you have several things going on:
 
Any time you destructively process just part of a clip, a new file is written for that section of the track to reference. The original file remains intact, and that section is just ignored. If you go to Associated Files in clip properties, you'll see the clip referencing more than one file, and nothing is done to consolidate files when you Save As unless they aren't referenced at all in the project, in which case they wont be copied to the new location.
 
Similarly, if you have un-bounced, non-destructive slip-edits that cause SONAR to ignore parts of files during playback, those non-destructive edits are preserved in the copy of the project and the files will not be any smaller.
 
But the above won't make a copy of the project bigger than the original project. I'm guessing where that's happening is that when you Split a clip, you end up with two slip-edited clips referencing the same file. If you then Save As to a new location with 'one file per clip' enabled, you're going to get a full-length copy of the file for each clip with slip-editing preserved in the clip properties. If you've done a lot of comping or other splitting, that's going to create a lot of redundant file content.
 
'One file per clip' is disabled by default, and should really only be used if all the edits have been applied destructively, and you have a need to handle clips as separate files (e.g. you're going to import individual parts into some other app).