GOG has created something of a problem for the Downloader
The Walking Dead Michelonne
When you talk about "Downloader", are you talking about the old GOG Downloader client (which is nowadays unsupported), or the gogrepo.py download tool that this thread is about?
I don't have any of those three games so I can't check if this would be a problem for gogrepo, but my understanding is that it is not
a problem (for gogrepo).
My faint understanding (without checking the script itself) is that just before gogrepo starts the download process, it quickly cross-checks whether the files you have already downloaded have the same filename, and the exact same size, as what is available in the GOG servers (according to the manifest file). If either one is incorrect, it downloads the whole file all over again.
So, if GOG has a file that has the exact same name as before but different size, gogrepo simply redownloads the whole file. No problem. I actually presume this is quite often the case with Game Goodies, e.g. if some manual zip file has changed, its filename is not necessarily changed, only the size may change (albeit GOG seems to quite often change the filename too at the same time, but there is no version numbering for Game Goodies).
If it happened that the new file had the exact same filename and size as the old file you already have, I guess gogrepo would (incorrectly) just think you have the new file already, and skip downloading it. However, when you run "gogrepo verify", then that wrong file would be caught as it still has the wrong md5 checksum (regardless of its correct name and size), and after that it could be redownloaded.
(except for maybe game goodies, as they don't have md5 checksums...)