"Take a mark/marker and remain in service" means the company gets credit for the run, but no longer needs to respond. Back in the day each company would keep a record of runs with them in the rig, and would make a "mark" on the paper, hence the term.
As for why the companies were assigned to the box then returned to service, it's because they usually have enough companies to handle the situation already. If additional companies were already assigned before the situation was downgraded, they'll be sent home.
One thing to realize and remember about listening to FDNY is that you're not actually hearing the companies being "dispatched" on the radio, per se. If they were in quarters, they were already assigned to the box about a minute or so before you hear the dispatcher announce the run over the air.
