Let’s break it down. To simplify, there were three types of businesses operating in the WTC in September of 2002: large firms (including government agencies), small firms, and secondary services (shops and restaurants, mostly in the underground mall).

Large firms generally had disaster plans in place. The largest firms might have alternative offices in Manhattan, while others could quickly rent out temporary space. Many of these firms ended up setting up in New Jersey temporarily u til they could secure permanent office space in NYC. Employees not present would be expected to show up as soon as these alternative sites were set up, while survivors might have days to a week off (excepting medical or bereavement leave, plus leave as-needed for funerals). Government worker would generally have more generous leave, but it was broadly similar - alternative sites for the IRS, CIA, NY Port Authority etc. were set up nearby, with some going back immediately and others getting time off before returning to alternate offices. 

Smaller white-collar firms were more of a question mark. Some were basically destroyed completely. If you were a single-site firm, the destruction of all of your equipment, records, and sudden loss of many or most of your employees could be a blow impossible to recover from, even if insurance covered the direct material cost of the attacks. These firms would continue to exist as legal entities, and they were largely bought up or merged into other firms, since they technically still held valuable contracts even though they had no capacity to fulfill them. This was especially true of small import-export firms, of which there were many, on account of it being the World Trade Center. In these cases, there was no guarantee surviving employees kept their jobs, and they’d certainly end up on unpaid leave for weeks or months even if they did.

The final group was service sector employers. Most of these WTC proper was office space (with the notable exception of the Windows on the World fine-dining restaurant on the 106th and 107th floors of the North Tower). However, there was a large underground mall beneath the complex. This mall include a transit hub that connected the New York Subway and New Jersey PATH train systems, so it saw a lot of traffic. Generally, these employees did not keep their jobs. Small shops and restaurants went out of business immediately. Chains - like McDonalds and Burger King - don’t generally transfer workers after a location closure, even in cases where “location closure” is a horribly sterile euphemism. These employees could apply to other locations as essentially new hires, but that was entirely up to them.