Empty System Working Set isnt dangerous. Not sure why you think that. My Cleanmem tool uses it and I run it on every system all day every day.
The Windows memory manager does all the work, the Empty System Working Set api is simply the call to windows to do the job. The used memory is moved into the standby list which is still in memory and the programs have back what they use instantly, this is why it is so fast, it is still in memory. Then memory not reclaimed is left in standby for a bit by windows, then when enough time has passed the meory is free.
Windows may move a small amount to the page file, talking only a few MB, as windows sees fit. Again Windows is controlling all this.
This has nothing to do with the file system.
Shane