1:
The reason the skiplist option was removed from tools is because it caused some confusion and it didn't work as I intended it to, as did the anti-idle option. There were conflicts between it and the per-site setting.
2:
If I understand your situation correctly then I think the ideal solution would be to change the skiplist settings 'When to skip' to 'automatic file transfers'
This will allow you to manually queue a file that would be normally skipped.
Then when you transfer a folder the only content of that folder will be applied to the skiplist.
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