I was having the same problem and just found a solution.
In my case, I had a 250gb hidden folder used by the Mail app filled with what was likely just runaway draft messages. If you use IMAP for a Google or Gmail account, this could be your issue as well.
First, in Mail, delete all the Drafts for that email account. Then, to prevent this in the future, go to the preferences for that account in Mail and change the Mailbox Behavior for Drafts to "On My Mac".
Quit Mail.
Then, use OmniDiskSweeper, free download from the highly reputable OmniGroup, https://www.omnigroup.com/more
After you open from the Finder though. Quit and open it again using Terminal so that it will have permission to look inside hidden folders. In Terminal and type:
sudo /Applications/OmniDiskSweeper.app/Contents/MacOS/OmniDiskSweeper
Then in OmniDiskSweeper, select the drive and click "Sweep"
After the sweep, I was able to drill down through the biggest folders along this path:
[user]/Library/Mail/V5/B83...(long code)/[Gmail].mbox/Drafts.mbox/4D3......(long code)/Data/
Inside that "Data" folder is a set of folders named with a single numeral (e.g., "0"). I think there were nine or ten. And within them, there was 250gb worth of coded files ending in ".emlx" scattered deeply through uncountable more single numeral folders.
To be safe, what I did was open that Data folder in the finder (there's a button in OmniDiskSweeper. Then in the Finder, open each one of the numeral folders which it contained. So I had nine or ten open single numeral folder windows (actually I did it in Finder tabs).
I then selected and trashed the contents of each one of those single numeral folders under Data. Literally millions of .emlx files and their folders.
Once I was done. I re-indexed spotlight via terminal: "sudo mdutil -i on /" waited an hour then restarted. After another hour or two, the Storage graph under About this Mac confirmed it. I had cleared 250gb of space with nothing lost (except maybe some old email drafts).
Hope this helps.