Can the employees use the documentary in legal situations?

I guess I'll turn this into an answer, though I think Flater gave a pretty good answer to the actual question as posed.

I don't want to dig too much into the first question. I'm not sure if they could use the documentary in a legal situation; but I would definitely be reluctant to go back on a verbal contract when it was recorded on video; regardless who the rights belong to. It would take some very specific documentary contract wording to be sure that the video couldn't come back to bite you.

What's to stop Dunder Mifflin from changing the agreement?

David argued against the terms, because it would cost DM millions of dollars.

Dunder Mifflin wouldn't want to change the contract. It was DM's idea to buy out The Michael Scott Paper Company.

When David Wallace protested the million dollar buyout, he mentioned something along the lines of TMSPC not being worth that much. Michael then spilled the beans that his company was worth nothing. Michael then made it clear that even when TMSPC goes bankrupt, he will just create another paper company to take DM clients, and another after that; because he has "no shortage of names".

This is when David Wallace agrees to the buyout, only after discovering that TMSPC is worthless. Either side trying to change the agreement wouldn't be beneficial at this point. DM wants TMSPC off their back, and TMSPC employees just want stable jobs. By the time the deal is made, David Wallace has about as much information as the viewer, and still decides to go through with it. There's no real reason in the show for him to back out.

What's to stop Dunder Mifflin from changing the agreement?

What's to stop Dunder Mifflin from changing the agreement even if either party takes notes? The note taking doesn't make a difference.

The only thing that matters is the contract that TMPC and DM sign - which doesn't happen on screen but there is no reason to believe that the contract was any different from the agreement.

Cinematographically, there's nothing interesting about showing both the meeting and a reading of the contract, if both contain the same information.

Is there any canon or official source that can confirm if the footage of the agreement was used to support Michael, Ryan, and Pam, or if the footage can be used in legal situations?

There is no confirmation on the agreement between DM and the documentary makers, so this cannot be answered in-universe.

If you want a real-world answer, this is better asked over at Law.SE, assuming that there is existing legislature that can override the specifics of the agreement between DM and the documentary makers.