System Data > 600 GB, Size of sum of files < 400 GB, where are the 200 GB?

There is Purgeable Space and there is Empty Space.

Purgeable Space which is Controlled by the Operating System.

When the Operating Systems decides the computer needs additional Empty Space, it will move a portion of the Purgeable to Empty space

AFAIK - there is no User Actions to hasten this transition from Purgeable to Empty Space

It can day or longer before this will occur.

The links below will assist in identifying what is taking up space on the Internal Drive and provide possible ways to remove data that is under the direct control of the User ( Home Folder ) . 

Rebuild the Spotlight index on your Mac

What is “Other” storage on a Mac, and how can I clean it out?

Free up storage space on your Mac

OmniDiskSweeper Safe to use

GrandPerspective 

➡️ How to delete Time Machine snapshots on your Mac.  

Often caused if the Time Machine Drive has not been attached  to the computer and TM Backup is set to run on a Schedule. 

TM Backup will make Snap Shot on the Internal Drive awaiting the TM Backup Drive to be attached. 

Only then will the Snaps Shots be transferred to the External Drive and deleted the Internal Drive. ⬅️

See used and available storage space on your Mac

Locate backups of your iPhone, iPad, and iPod touch

Notation - If the user is using a cloning software like Carbon Copy Cloner - suggest tweaking the Safety Net Feature in this software. It may be making additional Snap Shots that are not being Cloned to the Eternal Drive. If this should be the case, these Snap Shot could be using additional space on the drive 

The final word from Apple on Managing the " Other/ System Data “ Category

Other / System Data: Contains files that don’t fall into the categories listed here. This category primarily includes files and data used by the system, such as log files, caches, VM files, and other runtime system resources. Also included are temporary files, fonts, app support files, and plug-ins. You can't manage the contents of this category. The contents are managed by macOS, and the category varies in size depending on the current state of your Mac.

Unlike other people commenting on other forums, I would say System Data can be partially cleared up, I used Daisy Disk (I am not affiliate at all, I just find it not-expensive), it allowed me to delete cache files, files stored in messages and email that I sometime read but now they were just all data stored on my Mac, also I could see which were the big files that were downloaded into the HD so I could go and offload them (Remove Download). That in summary reduced my System Data from 150GB to 75GB and the total data from 235GB to 115GB which was just amazing considering it took me 30min to do it.

Note: I didn't delete small files, just the largest ones, if I keep deleting I am sure it can be reduced a few GBs more. I have a MacBook Air M1. The only files the app could not show were "Hidden Files" or containers, but that wasn't a major problem for me since it was only 11GB.

BTW: I am not sure where the 200GB are, just wrote this note for those who struggle with HD free space.

Hope this helps.

Hoinx wrote:

Using tools like Disk Inventory X I sum up the space used by the files / folders listed to approx 340 GB. That's the same the Finder lists when calculating all sizes, including hidden user Libraries etc.

Those disk scanning tools don't understand modern macOS file systems. Don't use them. At best, they will give you misleading information. At worst, they will lead you to deleting important data.

What is using up the missing > 200 GB?

These are probably local snapshots.

How can I free the space?

Wait. Local snapshots will be automatically deleted after 24-48 hours. Most people discover this when they try to download some update and it fails.

With the current state of misinformation on the internet, a failure to download the latest update is considered by most people to be a critical, life-changing event. So, they call in sick to work and spend all day with those disk scanning tools deleting critical files. After a few hours of work deleting files that aren't backed up, they have even less free storage than they started with! That's because those local snapshots are keeping the files on disk for another day. Eventually the system will purge these snapshots and the storage will be recovered.

But once you get into this state, there is no amount of deleting that will suffice. You've run out of storage. That's the sad fact. You can buy an external hard drive and archive your files. You can delete old files that you no longer need, as long as you make sure they are document files that you created. If you use those disk scanning tools, they will give you easy access to internal app files that you shouldn't be deleting. If all your storage is taken up by Photos or Music, user documents, then you might be able to recover some storage by turning on all iCloud optimization options, and paying a monthly fee.

Either it took a while for the change in Spotlight to have an effect, or there was something with that other user account which had some clean up to do. Or maybe it was a combination.

Thanks for the follow up as we will need to remember to have people access each of the other macOS user accounts next time.

Hoinx wrote:

Yesterday I excluded the whole Macintosh HD from Spotlight, restarted, still no improvement, only approx 20 GB gained.

That is not going to do anything to recovery any storage. It is just going to make your life miserable for a long time to come.

Yes please do work through the original reply at your own pace.

We are here to offer additional assistance if required

You are welcome and thank you too