Here's the dialogue in Tolwyns office:
Tolwyn: Ah, law and order – concepts that seem to be crumbling throughout the Confederation.
Maverick: These are transitional times, Admiral.
Tolwyn: Yes, but in the Kilrathi, we had a common enemy. It was Humanity’s finest hour. Now we cast about, uncertain. Well, you’ve seen it for yourself, the wanton destruction. That’s why Confed needs your services – your experience – again.
Maverick: You know where my loyalties have always been, sir.
Tolwyn: Something we count on, Colonel. For the past months now, there’s been an undeclared war waged against us – acts of terrorism, piracy, sabotage. Is it symptomatic of these transitional times or is there something else at work here?
Maverick: Do you see a strategy or design behind it?
Tolwyn: Every time I connect the dots, I’m always guided back to our long-time allies in the Border Worlds.
Maverick: And you think they’ve undertaken some kind of guerilla war?
Tolwyn: Well, their relationship with Confed has always been uneasy. The price of freedom is eternal vigilance.
Maverick: Which is where I come in?
Tolwyn: Hm. Well, we have a long history together – one that, uh, I daresay has been a bit rocky in the past.
Maverick: We have had our differences, sir.
Tolwyn: But there’s no denying our achievements. Which is why I have personally reinstated you to active duty. Not only will you be my eyes and ears, but your very presence in the Border Worlds will send a potent message to all the galaxy.
Maverick: I am no politician, sir.
Tolwyn: Actions speak louder than words, Colonel. I’m not sending you there merely as a symbol. I’m putting you back in the cockpit, where you’ll be reunited with an old friend… the thrill of battle.
From that you can guess at at least three motvations:
1. He wants to use Blair's popularity as a tool for his own political agenda
2. He still values Blair's flying skills, and wants to use them to tilt the conflict into the direction he desires.
3. He wants to use Blair as "eyes and ears", which may be to simply collect information, or to monitor his own skill in hiding his actions and motivations. The latter would be really smart - use your enemy to see if he detects that your conspiring.