To be clear, I'm not slamming iCleaner. This is just a means to record the steps that lead to this problem.

After completing iCleaner's cleaning task, the phone resprings, but fails and somehow enters Safe Mode. In Safe Mode I'm at the screen where it was asking the typical questions that are asked when setting up an iPhone for the first time. (EG, Language, region, wifi network, etc). All the while it was asking that, the line "Exit Safe Mode" was at the top of my screen. I tapped it numerous times, but it didn't work. Then I decided to force-reboot the iPhone thinking it'll correct... It didn't. Rebooting the phone now leads to a all-white screen that says "press home to upgrade" at the bottom. This is where I'm at now.

What can I do? I want to keep this phone on 10.3.1. How did this trigger from using iCleaner? I've used iCleaner before with no issues and I didn't change any cleaning settings for this run. How did this happen this time?

12/14/2021 Edit:

To anyone who's been following this, I have some updates.

Namely, I can access the home menu now and my SE's still on 10.3.1. I decided to let it "update" and it retained the iOS version. Although, I'm having issues signing in with Apple ID when stocked. But after I use TotallyNotSpyware, I can sign in.

Also, I reached out to some Jailbreak gurus and together we discovered how iCleaner did it. The toggle "Custom files and folders" was enabled with var/mobile/ being the target directory. These combined impacted my device.

Now the next step is to try to recover what I can. Thankfully Test Mode was enabled and I do indeed have a mobile.iCleanerBackup folder in place. Inspecting the contents seemingly reveals that my user data is still present there.

However, choosing to restore from it hasn't yielded any actual results. Restoring backup files doesn't restore my lost data and this is where I am now. I'm not sure what the next steps are from here. I can access the folder directly and pick and choose things to pull out -- I got my photos and some audio clips, however I'm really needing some user app data such as my game saves, notes, contacts, etc. restored to their respective apps.

I will go to make a new thread detailing some ideas I've tried already. Maybe someone could suggest something I haven't tried. As of this thread, the mystery on how it happened has been solved. 🙃🙃