I don't think so (and they are showing fine here), that's why I'm confused 
Maybe go to Help => Export Diagnostic Debug Information and send that to andreas@folivora.ai, this would allow me to reproduce your exact setup.
I will send that right away. Yes it is quite strange and you would expect it to happen on all systems if a path or similar was broken with the update, but software is software....
Thanks!
Unfortunately even with your exact setup it seems to show fine ;-(
I'm a bit out of ideas right now, let me do some tests.
Thanks, I will remove and reinstall an older version and use a backup I have from before I upgraded macos and report back
BTT automatically keeps backups for the last few versions in ~/Library/Application Support/BetterTouchTool, just downgrading to the last version you had installed should go back to that backup. (the files in that folder can tell you which version that was exactly)
Are there any hidden files or caches I should delete to ensure I'm getting a true "re install"?
Ok I completely deleted BTT and restarted and then reinstalled a version from beginning of April. Everything started working fine. I got the pop up for a new version is available, reinstalled the alpha and the icons are gone again!
very weird. The new versions are built with the new Xcode, maybe there is some strange incompatibility with 10.15.3. I’ll have access to a 10.15.3 machine tomorrow and do some tests!
I have an xcode update available in app store 
that shouldn’t be relevant, but there have been various cases in the past were new xcode versions broke stuff on „older“ macOS versions. It’s only relevant for the build machine though
I will install it now just to see, its an unusual problem
Ok as expected Xcode update did nothing (as it shouldn't have).
I went back through all the old versions. The very last version that works is 352-1562
After that version 353-1562 breaks it. Coincidentally there was a large gap between these releases so perhaps a big change was made. Hope this info helps.
I'm not willing to try macos 10.15.4 again due to the garbage scrolling inertia changes (off topic but would love if BTT could provide a fix but it seems like they made a deep change as .GlobalPreferences.plist are still the same)
Interesting, what kind of change was there to inertia scrolling? (I haven't noticed yet)
Thanks for figuring out which version broke it. This was indeed when I upgraded to Xcode 11.4 (352 is still on 11.3.1, 353 is built on 11.4), so it seems quite likely that the issue is connected to the Apple frameworks / build tools.
No problem, it helps me as much as you.
It has not been documented what the changes were but the scrolling feels slower/ like an old windows trackpad / fingers in mud type feeling. Its widely reported/ complained about: https://www.reddit.com/r/MacOS/comments/fp7e5l/macos_10154_scrolling_behavior_has_changed/
I could not live with it or adjust after a few days of use (I use trackpad not a mouse)
Ah I'll look into that scrolling change. sounds like a bug to me, but maybe there are some internal flags that can restore the old behavior.
You could probably workaround the issue while keeping the latest BTT by using the icons from [v3 Update] Native Apple Touch Bar Icon Pack for BTT
I'll look into a workaround though.
I would buy BTT again if you could revert the scrolling changes 
For now I am just using the last version that works for me, I don't need the very latest features anyway. But just let me know if you want me to test a fix.
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One final observation. It appears the icons may actually be present but are the same colour as the background so seem invisible. When pressed the icons do appear under my finger but they are black not white. The grey background when pressed allows them to show.
Ah that's good to know and will make the workaround easier.
Possibly try 3.363 alpha, which will be online in a few minutes. I made a small change to the image assignment, not sure whether it will make a difference. But it's not that important, I'll myself do tests on 10.15.3 tomorrow.
No change with that alpha i'm afraid
@Andreas_Hegenberg Made a few changes to my touchbar and said i'd try the latest alpha, still the same problem (but I have moved to buttons now so no longer an issue for me). I noticed a bit of an odd bug/feature though. When I installed the latest alpha my touchbar config went back to when I was using widgets and had the problem in this post, undoing all my work since. This is not a problem as it was backed up but possibly the behaviour is a bit funky if you go from an alpha > older version > back to alpha.
I had a look in ~/Library/Application Support/ in case its an issue with the auto backups but there are no BTT files or folders in there, hidden or otherwise.