Launcher seems to treat files with the same name but in different locations as the same

I have been trying to update a manually-jaunched Fiji.app with the SciJava-Ops update site, which also ships an updated Jaunch. This has brought up some weirdness.

Here's what I did:

Download a jaunch bundle
Manually install it into a fresh local Fiji.app
Open Fiji and turn on the SciJava Ops update site

At this point, while ImageJ is still running, the updater seems to know that my launcher (fiji-windows-x64.exe) is different locally but doesn't offer to update it. The updater does not recognize that the files in the jaunch dir are different.

Try to complete the update. The new fiji-windows-x64.exe doesn't work, regardless if it's the manually installed version or if I told the updater to update it in step 3. If I did do the update in 3, I can get the new jauncher to work by removing/renaming the jaunch directory so that it properly finds config/jaunch.

==Path A==

Let's go forward assuming we did these things and have a working launcher. We also have a fiji-windows-x64.exe.old for the old launcher.
Now I run Fiji again and turn the SciJava Ops update site off.
This uninstalls everything as expected and leaves a pending update.
I have to run ImageJ-win64.exe to complete the update
Some how, when completing the update, my fiji-windows-x64.exe.old is deleted. But the updated version served from SciJava Ops remains!

==Path B==

If we didn't update the .exe and didn't rename/remove the jaunch directory, we have to use ImageJ-win64.exe as our launcher after the update.
Checking the updater after applying the update, we now get extensive "locally modified" warnings, including for the jaunch directory - however, the only option for them is to uninstall (reasonable, since the update site doesn't know about these files) while everything else can be updated:
After applying this update, the fiji-windows-x64.exe launcher still doesn't work because of the jaunch dir, which has to be renamed.
If we rename/remove the jaunch dir at this point, we are essentially harmonious with Path A above.

There are at least two points of confusion for me that seem like bugs:

The .old exe being deleted upon restart after turning SciJava Ops off
The updater calling the jaunch files "Locally modified" when they should be local-only.

I have to think more about this but wanted to get the steps that I took recorded here.

imagej / imagej-launcher

Launcher seems to treat files with the same name but in different locations as the same #97