“Well, it's nice to have you back.”

Your coworker took off work for 6 weeks for maternity leave. She returned to work this week, and you just saw her and talked to her for the first time. You're finishing your small talk, so you say:

Well, it's nice to have you back.

Well...

You use "well" to change the topic of a conversation or to signal the end of a conversation. In the example above, the speaker uses "well" to show that she's ready to end the conversation.

It's nice to have you back.

This is a set expression that people say when someone returns from a vacation, sickness, etc.