Then I guess I'm stuck, because I doubt that stuff can be messed with manually. I wish I had another 3DS to do a system transfer to, THEN format.
Assuming the downgrade completes successfully, O3DS systems should not have the problem that arises with N3DS systems. This is due to the nature of how updates are handled on the 3DS system. Essentially all updates are cumulative. Each and every update package includes all updates that were done previously as well. The problem with the N3DS is that because it shipped with updated versions of almost every titled, many of them are not included in further updates because they were already up to date. This is why the N3DS 9.0 package has 102 titles, while the O3DS package has over 120.
Basically trying to actually downgrade a N3DS to 9.0 or 9.2 with an update package is effectively the same thing as trying to downgrade an O3DS to 2.0. It is not just a matter of installing older versions, there are also titles that don't belong.
The best way I can think of to describe it is like this:
You have a device that ships new with a total of 10 programs installed. The first update package (2.0) installs 4 titles. 3 of these are updates and the 4th installs an 11th program as well. The second update (3.0) contains 10 titles. Of these, 4 are new titles, bringing the system total to 15, and another 2 are updates to the 1.0 versions. The remaining 4 are the exact same as the previous update. They had to be included though or users would have to install 2.0 and THEN 3.0.
Now lets say a user wanted to downgrade their device back to its 2.0 state. They can't just reinstall the 2.0 update and call it a day, because 3.0 introduced 4 brand new titles that were not there in 2.0.
So you begin to see where problems arise?
Now lets take it a step further and release a hardware revision of the device. It ships with the 3.0 updated titles already installed, plus a few of them are specially written for the hardware revision. Then you release a 4.0 update. This update does nothing more than update 2 existing titles. No new ones are added. Because of the hardware revision that required unique versions of some titles, you have to release two separate update packages. But you also know that the new hardware already has the 3.0 versions, so that package only gets the 2 titles that need updating, while the old hardware gets a package with every title that has been updated.
This is what has happened with the N3DS. The earliest factory revision of the N3DS shipped with 8.1 iirc (also only in Japan, but that's irrelevant), so when 9.0 was released, the N3DS package ONLY included the titles that got updated from 8.1 to 9.0, where the O3DS package contained a cumulative collection of all titles updated since 2.0.
Now the research I did into the installed title list on a N3DS that shipped with 9.0 show that there are 2 titles that did not get updated in from 9.0 (the first update for the N3DS) but that did get updated later. So now we see why trying to downgrade a N3DS to 9.0/9.2 with JUST an update package is like trying to downgrade an O3DS to 2.0 with JUST an update package. It won't work right.
Now as to why you, with an O3DS, are having problems, I do have an idea. There are a total of 4 titles (if my memory is correct) that were installed to the O3DS with 9.3 that were not present before. They should not cause problems, but I suppose it IS possible they are the root of your problem. I will see if I can track down those title IDs for you, but I may have listed them earlier in the thread. Basically its the nfc/amiibo stuff.
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@Captain Skank
Assuming you region is USA, try uninstalling these titles:
0004013000004002
0004001B00019002
0004003000009E02
If your system is not a USA region system, just let me know what region it is and I will get you the IDs you need to uninstall.