They didn't remove the content. They'd disable a link and share a new one to the same file.
It's sort of a loose way of complying with the DMCA requests.
When someone uploaded something that was already in their system, their system recognized it as something that didn't need to be reuploaded, and just pretended to upload it while it gave the user a fresh link.
If a copyright holder found a Megaupload link to some of their stuff on a piracy site, they could report it to Megaupload and the link would be terminated immediately. I'm not sure if it really matters if the file wasn't purged from Megaupload's system immediately. If the link to the file is dead, nobody can access it. I'm sure they had a system for purging files that have no links (IIRC, if the file wasn't accessed in x number of days, it would automatically delete). Megaupload could have done more to fight piracy, like discovering and deactivating any and all links associated with a heavily-pirated file, or purging the pirated file immediately once the link was reported, but from the perspectives of both the pirates and the copyright holders, Megaupload
seemed to be complying with DMCA takedown requests.
And they weren't just "disabling links and then sharing new ones", as that implies that they were sending secret messages and willfully trying to undermine DMCA takedowns. They would share a new link only when a pirate made a fresh attempt to upload a taken-down file, and at that point, it really doesn't matter if Megaupload was lazy in taking down the original. If they had taken it down, it would be back up again.
Legally speaking, getting lazy and keeping the file uploaded and merely trading in active/inactive links while people were shouting "Put this up!" "Take this down!" "Put this up!" "Take this down!" is going to screw Kim Dotcom, but it doesn't seem like
that bad of an idea. It just seems like they're screwing him on a technicality, since he's Kim Dotcom, founder of Megaupload, and they were desperate to find
something to pin on him.
Don't think Kim is affiliated with MEGA anymore, they had some sort of falling out some time ago.
IIRC, he restarted the company and tried to make it lawsuit-proof, and then since he was facing these legal troubles he put it all in the name of his beautiful trophy wife.
Then his beautiful trophy wife said "Thanks hon, but I only ever loved you for your money, and now you have given it to me. Bye!"