Trying that now. I had the idea this was a simple operation, something I will need to inform users that use my code also about.
EDIT: This works as planned !
If you’re using the platform = teensy directive in the platformio.ini as you showed in the comment that’s the main issue. With that you’re saying you want to use the stable platform (still at 1.53), you must use updated git version with platform = https://github.com/platformio/platform-teensy.git (for now, until it’s not yet released as stable) to get the platform version using the new package
Well I had tried that directly after doing the pio upgrade teensy. But this had no effect, the removal of the .platformio subdirs did work as explained.
Do you have git installed?
Have you tried opening a CLI and doing a pio upgrade --dev to upgrade the PlatformIO core?
Installing git did the trick, thanks allot man!
Do you know how long until PlatformIO updates TeensyDuino to 1.54?
The one you have on your git is no longer the beta right, it’s 1.54?
I don’t know since I’m not staff, but from experience they’ll first wait a bit after putting it into the dev branch (to see if people directly have any problems with it), then it gets published as stable. Give it maybe another week.
I’ve just updated it to contain the 1.54 release version, before that is was containing 1.54 beta #12 (last beta before stable release).
Would it be possible to update to latest Teensyduino 1.57 release 
?