Hi @JulianJo
I have referred the steps that you mentioned in problem statement associated with both folder and file , that I uploaded from OneDrive to the Z: Drive created by the desktop app.
I noticed file and folder both are showing up in the AEM web application after the green checkmark with 'Available locally' began to appear for files as shown below -

Could you please check the cacheinfo.json file inside relevant path.
Please refer the following document to troubleshoot - : https://experienceleague.adobe.com/en/docs/experience-manager-desktop-app/using/troubleshoot
Some additional information , I have tested this scenario with Adobe Experience Manager 2025.3.20133.20250325T063357Z-250300 and Windows 64-bit Enterprise (v3.0.1) Desktop app.
Thanks,
Debal Das