(I could probably go into more detail on this, but it's already taken me an hour to write so this'll do for now.)
tl;dr: How can the humans win? With great difficulty.
What troubles would the human colonists encounter while fighting against them?
Your reptilians are shapeshifters. Ever seen The Thing? Shapeshifters are not only really difficult to fight, they're also bloody terrifying.
Consider a simple one-on-one skirmish between a human and a reptilian. The reptilian could turn into a mosquito, making him impossible to shoot (and potentially allowing him to infect the colonist with space malaria). He could turn into [insert whatever giant deadly predators your alien planet has]. He could turn into a sobbing human child, begging the soldier not to shoot, and while he wrestles with his conscience, another reptilian sneaks up and shoots him in the back.
Then you'd have reptilians disguising themselves as human commanders and giving phony orders, or disguising themselves as refugees/soldiers to infiltrate the colonists' camps, or turning into small animals to listen in on covert meetings (like a literal fly-on-the-wall), or turning into small animals to set up an ambush ("Hey, look at all those birds sitting up in that tree-- OH GOD THEY'RE ALL REPTILIANS")... you get the picture.
I once wrote a shapeshifter who could "heal" from injuries by simply shapeshifting into an uninjured form. If your shapeshifting reptilians can do the same thing, that's really bad news. You're looking at an army that outnumbers you by 3 to 1, can heal from just about any physical injury that isn't immediately fatal, and can be anywhere or anyone or anything at any time. I repeat: bloody terrifying.
So how can the humans win?
Well, if there isn't already a way for the colonists to tell who's human and who's reptilian (infrared, DNA scanning), they'll come up with one very quickly. Perhaps a system of ever-changing passcodes,
or that old trick of asking questions that only the real person would be able to answer. @Draco18s suggested in a comments that every colonist be given a VPN dongle, and that gave me the idea of going one step further: an ID chip embedded under the skin. It would be difficult for the reptilians to replicate such a thing.
Once you've got the ID problem sorted, hold any and all important tactical meetings aboard one of your orbital spaceships. If you suspect someone's secretly a reptilian, fire them out the airlock. Heck, you could fight deception with deception: hold fake tactical meetings out in the open, knowing that the reptilians will eavesdrop on them, while holding your actual meetings up on your ship. The reptilians will act on the false info you give them, and then you can take advantage to plan surprise attacks of your own.
Finally, if you still can't overcome the reptilians' shapeshifting abilities or sheer numbers, just go down the scorched earth route: burn the forest down. Nuke it from orbit. You said in a comment that you didn't want to do this because it would render the land unusable, but in warfare there eventually comes a point where you really just don't care about things like that anymore: you just want to win.