In my case, Linode opened an “AUP violation” ticket with a copy of the report, the steps they required to close the ticket (essentially: fix it and explain corrective measures), and a time when they would disable the server otherwise (which was something like 24 hours). It sounds like itch.io decided to ignore the AUP violation ticket and their server was disabled after 24 hours, just like the ticket said it would. (Waiting on a support ticket instead of calling also seems like a weird bad choice when your whole site is offline.)
I guess, having some first-hand experience with Linode’s malware handling process, that itch.io were at fault here, but I guess there may be more to the story they haven’t shared or weren’t clear on.
[0] Actually twice; some internet vigilante hooked up a virus scanner to a web crawler and was sending false positive reports directly to the abuse address for the netblock. After the second one I kindly suggested Linode stop accepting these reports, and never heard anything again.