My browser / operating system: ChromeOS 13904.22.0, Chrome 91.0.4472.33, No Flash version detected

That's normal: the project data limit is 10Mb. Anything bigger than that won't save.

These 3 lists combined are less than 10MiB (It's too bad they lowered the max from 50 to 10 in 3.0)

Some clarification is needed here: There is no limit on the overall size of the project anymore. Instead, there is a 10 MB limit on the size of assets, and a 5,250,000 byte (~5.007 MiB) limit on the size of the JSON file that stores the project's code.

In addition, the format used to store the lists in Scratch 3.0 is rather inefficient, storing two redundant copies of the list (I believe one is the actual data and one is for the on-screen monitor). Along with that, each item adds about 4 bytes of overhead - so it takes less than 2.5 MiB of list data to cause a project to not save.

I should note that Scratch 3.0's 200,000 item limit on lists would make gbc.sb2 essentially useless for all but the tiniest of Game Boy games. You would be much better off using this tool to download the original .sb2 file and editing it in the Scratch 2.0 offline editor - but you're on a Chromebook, so I guess you're just screwed. (I also should note that projects uploaded from old versions of Scratch stay in their original format - so, for example, you could do whatever you wanted to gbc.sb2 in the Scratch 2.0 editor, use that to upload it to Scratch, and then play it in Phosphorus without any issues.)