Just be gentle as you can because, depending on what you're doing next, you may need to 'fill' in the damaged areas. After removing ALL the tiles, then assuming you're reinstalling stick-down tiles, you'll want to install a layer of Lauan. THis way, you WON'T damage the sub-floor in the future (assuming you have to do this again.) The Lauan is really cheap and perfect for this scenario. Of course, 1/4" Lauan will add that much 'height' to your room. You may find that doors and Room Transitions will either be 'off' or something like that. PLUS, you may need to trim-out the room, perhaps on all the walls or under cabinets, and/or the like.
I wish I had more to offer. My best to ya and hope this helps.