What is kept when doing an "in-place upgrade" and choosing not to keep apps (only personal data)

What is kept when doing an "in-place upgrade" and choosing not to keep apps (only personal data)?
A standard "in-place upgrade" fails to repair my Windows 11 (get an error in SAFE_OS BOOT phase).
So I'm thinking about doing an upgrade only keeping data (not apps) to see if that works.
But what data is kept? Is guess Documents, Pictures and Videoes. But what about data in "Roaming"?
Lots og apps have started to keep data in the roaming profile. Will does data be kept also?
Or will I need to restore them from a backup? And what abaout data in "Programdata" folder?

Read this: Will upgrading from Windows 10 to 11 delete my files and apps? | Microsoft Community Hub

In-place upgrade is to use to replace the current operating system files on your computer. Unlike a clean installation of Windows, you can start a Windows in-place upgrade when your OS is still running. And an in-place upgrade can keep your files, settings, & apps during the upgrade process. You can perform a Windows 11 in-place upgrade is to use the Windows 11 Media Creation Tool. Make sure to select Upgrade this PC now and click Next. Follow the on-screen guide to perform a Windows 11 in-place upgrade.

Another possible route is that you tell the problem you have if you don't know a fix. Maybe it has a "surgical" solution known by someone. If you're sure it's in the OS, maybe DISM restorehealth and SFC.

Imo to answer your question precisely you have to be expert in OS data structures and the registry.

"Failing items" can be files (like the ones in the folders you mention) and/or registry keys. The registry is somewhat "opaque" for my taste, and it's "special" in many ways compared to a mere collection of regular NTFS files that could theoretically hold the same info, although this kind of "database" can be less efficient, and it's the sw maker who does the design, not the user.

Any item or collection of them can be affected by, in increasing order of severity, "internal bugs" (functionality flaws that only affect the item itself and maybe other non-OS items, not the OS), "prohibition" by the OS (although it can work from a "mechanical" standpoint if it's in good condition and you manage to trick the OS), incompatibility with the OS (it needs interfaces or resources neither present nor installable), and corruption (some bits, texts, etc that compose the item have been randomly altered by a hw error -most times silent, RAM is a frequent culprit of this and it can also happen with good quality hw that is in good condition, it's just less frequent- or a sw bug).

Many years ago I could "demonstrate" myself that my (old version) OS install had corruption and/or bugs beyond repair. To be exact beyond "economic" or "with reasonable or available means" including my own knowledge. This is quite subjective but somebody has to do a decision. Corruption in the registry is a common cause of this.

A potential problem I see in the repair install method is that it does a somewhat unnecessary audit that can fail for reasons different from the problem you have, even if they're "good" reasons, and such a failure is very opaque. For example this old failure (caused by an OS bug if you ask me, currently fixed afaik) prevented me from upgrading to 24H2 until I was able to detect it somewhat coincidentally.

Another matter is that an OS and the user can tolerate corrupted, and/or wish incompatible or "forbidden" items, that may cause non critical glitches or none at all, but the "install audit" may fail for them or forbid them. Messages (see our fantastic 7 PB of logs, kidding of course :) ), causes etc can be very opaque. This can be for the difficulty in associating a low-level item that has an error with the high-level item that the user can manage.