We have an old bush that gets the job done. Just recently dad ran over a root and the blade is now slightly hitting the deck as you run it. When cutting light brush and heavy grass it seems to hit the deck more. We have not worried about it but now there at a couple of small holes in the deck.

I lifted the bush hog up and spun the blade. It appears to be 2" from hitting anything. The blades do slant slightly upward though.

Only thing I know to do is take the blades off, bend them to where they are flat. Have the small holes welded up.

It just seems odd that the blades don't hit when I spin it by hand but do when spun by the tractor.

I don't know what question to ask here, so just give me some input. We are not experienced with farm equipment very much.

Sounds like the gear box mount is flexing when under load. When you get into some heavy grass or whatever, it causes resistance and that's where your torque comes from.
Just a guess. Take a look at how rigid or flimsy the metal is where the gear box is mounted.

^^^ This. The only other explanation would be your lower bearings in the gearbox going out and allowing the shaft and blade pan to move around. You can push up on the edge of the blade pan (or bar) with some force and see if there's any movement up an down. If there is, the gearbox needs repair ASAP. The mount can PROBABLY be beefed up by a GOOD welding and fabrication shop, but figure on a couple hundred $ at least. If you do that, have them beat the groove the blades cut in the deck back down and weld them closed.

Do not DO NOT try to heat or bend the blades. This will take the temper out of the metal and may make them brittle.

A large chunk of broken blade coming out for under that cutter while they're spinning full speed could have disastrous (if not deadly) results. Be VERY careful with a bush hog.

You might as well replace the blades also. you can get them at Tractor Supply. Not too expensive.

Change the blades before doing anything else.

With new bolts

the stump jumper is probably bent

Could be ........loose gearbox, loose stump jumper, warped blades, warped deck, warped shaft or any combination of these. Cutting rocks and big hardwood stumps will cause the above.

When I first read it I was thinking the same thing as fuzzy and TC. The new bolts part is important.