EDIT 12/2/2019
After even more testing, I discovered additional issues. STLink utility works and recognizes the device, allowing to program other STM32 chips. The older Atollic Studio can use the franken-Stlinkv2-1 to debug, without problems
Unfortunately STM32CubeIDE, which is the development environment ST now supports, always checks the STLink version before starting, and a modified clone doesn't work, because it is not recognized as an STLink when checking the type (same as the STLink update utility not recognizing the device). So if you use STM32CubeIDE, you won't be able to use this hack
On the positive side, the virtual serial port works just fine (STM32+Audio firmware)
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I did a few more tests.
I have an old copy of the ST link upgrade utility from February. This is the last "fully working" version I have, and even the STM32+MSD+VCP can fit in 64k devices. You can still download en.stsw-link007_V2-32-22 from the ST website (as of yesterday) and it works, but in that version, the STM32+MSD+VCP is too big to fit, so can only flash STM32+Audio, which in any case provided a VCP port. The flash ends with a "failure exiting upgrade mode (Error 1)", which I suspect is due to the lack of a USB renumeration hardware. But simply removing and reinserting the ST link, works and recognizes the STLink plus VCP
Instead of using the EXE I tried using the jar file provided in the "AllPlatforms" directory. A jar file can be opened with any zip utility. I opened STLinkUpgrade.jar\com\st\stlinkupgrade\core\, to find all the f?_?.bin files. Replaced the files in the en.stsw-link007_V2-32-22 jar file with the same binaries from the last downloadable jar utility. Since the en.stsw-link007_V2-32-22 and the latest version use the same encryption, I now have a working ST Link 2.1 from a cheap eBay clone, with the latest firmware and VCP. Caveat: I have not soldered the necessary bodge wires to actually test the VCP, but the ST Link portion works fine, so I have no reason to think that the VCP won't
I also tried using the very old version from February and copy the latest f?_?.bin files, but I think that one and the new one have a different encryption, and did not work. The STLinkUpgrade.jar from en.stsw-link007_V2-32-22 plus latest bin files from the most recent jar file, seem to work fine
Clearly the same limitation as before apply: you need another St Link to flash the 2.1 booloader using the SWD interface of the target St Link, then use jar to update the target STLink. Once updated, the stlink upgrade utility cannot upgrade it anymore: it needs just the bootloader to be able to flash it (due to the missing USB renum circuitry)
So, if you are quick to download en.stsw-link007_V2-32-22 from the ST website before they remove it, you can update your STLink clone to 2.1 with VCP (not MSD, but personally I never found MSD to be that useful, so happy with just VCP (the weirdly named STM32+Audio)