Which settings are affected?

At least settings in:

• Build server integration (Jenkins) and
• Revision links.

Not immediately testable in all other settings that support this level (GitExtensions/Detailed, Plugins).
But at least the setting for Plugins/Plugin Manager is affected as well (not sure if this level even makes sense there 😄).

Revision links.

Not reproducible. These settings are applied on repo switch.

Plugins

... are not my specialty.

This concerns different braches and file content in the same repository location.
Cached internal state seems to include distributed GitExtensions.settings file (per repo) and never refreshed during runtime.

Having a matching cached entry in GitExtSettingsCache is likely responsible for hiding content changes.
At least distributed settings would need to be invalidated on manual refresh or when a branch change is detected.

GitExtensions restart required

This is not necessary. There are two workarounds:

• manual: Reopen the current repo, e.g. by selecting it again in the toolbar:

  

• event script: Create a non-background script (those trigger a refresh after their execution)

  

When testing this, I noticed that these workarounds are not necessary - at least for:

• revision links (URL changed in LinkFormats.GitExtLinkFormat.Format)
• build server integration (BuildServer.EnableIntegration = true/false)

So, which dedicated settings do you vary in different branches?
Do the workarounds help?

I do switch configuration of revision links in branches. ☺

But the condition to reproduce an issue has turned out to be more tricky than I thought;
Only one of of my branches had a GitExtensions.settings file!

• When starting up (initial load) of the branch without a settings file, no updates are triggered for that repo ever
• When started with and switching between branches that both have a settings file, everything works as expected
• When switching from a branch with a file to one without, the settings do not get cleared.

Thanks @mstv to getting back to me so I could get to the bottom of this. 😄
My guess is you tried variant 2, while I always managed to trigger 1 and/or 3 (up to my latest trials).

While the workarounds do not make a difference in the pathological states/changes, they are (of course) also not required in condition 2 (everythin is fine) here.
Interestingly, in any condition the expected state is shown correctly in Settings.
But it does not get applied in the commit graph or info views in the described problematic states and transitions.

Could you test please whether #11781 suffices?
https://ci.appveyor.com/api/buildjobs/njcx71af2ds04f4c/artifacts/artifacts%2FRelease%2Fpublish%2FGitExtensions-Portable-4.3.0.17846-4663b8621.zip

The change seems to remedy condition 1), since now event handling is always registered as per the patch.
However, when going to a branch without a file in 3), the settings still do not get cleared.

It seems there is still further change required to properly handle a disappearing file. 🤔
_fileWatcher.Deleted += … and maybe even some further action in LoadImpl (far off my area of expertise!)?