I just installed (April 9, 2021) a "Required Update" to Portable App which I keep on a flash drive and during the installation virtually all of my data files were deleted from the flash drive. I would be very careful with the update and recommend not installing it until a further explanation is provided by the software developer.
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Please provide some additional details including your operating system, full install path, etc. If you did a platform update (which was released back in September), are you sure it was installed to the same location? If you install it to a PortableApps sub directory (so Start.exe is inside there) it can get confused about what its root is. The platform update doesn't alter data files for any apps.
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