First, I cannot imagine this to be caused by WinSCP 5.x vs 6.x. If you believe otherwise, can you please try to downgrade and double check?

Anyway, you can exclude any files or folders you wish using File mask in Transfer settings:
https://winscp.net/eng/docs/ui_transfer_custom#other

Excluding hidden files is possible too, in the same place.

I use KeepUpToDate (minimised) in WinSCP to monitor folders edited by Visual Studio 2022 (v17.5.5) on Windows 10 64 bit.

It worked well in WinSCP versions 5.x but since upgrading to 6.1x (currently using 6.1.1) I am getting very frequent error messages like

System Error. Code: 32.
The process cannot access the file because it is being used by another process

The error usually relates to a write.lock file in a FileContentIndex sub sub folder of /.vs which seems to be a temporary file.

If I disable the subfolder option, that prevents the error, but that's not optimum because in most cases I also want the images folder, and often others, to be kept up to date too. Though I don't really want the /.vs subfolder to be copied to the public server, because I've no idea what else it might put in there,

Could there perhaps be a dropdown from the subfolder option, with checkboxes to allow only specific subfolders to be copied? Or perhaps an option to exclude folders that begin with a dot?