You need to be jail-broken for this

Open cydia and search for iFile or any other file manager

Then when in Ifile go to var/mobile/applications

Find flappy bird (Might have to enable show app names in your ifile settings)

Then go to Documents <-- I cant remember if its under flap.app or not

Open the file in there with the hex editor

The first four lines in the file are your high score

Google a decimal to hex converter and put the score you want into the decimal part

*Note: if its larger than four sets of 2 characters(ex:00) then it wont work*

Change Only the first four lines to the hexadecimal output it gave.

Then on the fifth line change it to 01

This does NOT change your game center score.
Also the highest legit score you can get by playing is 9999

If you want to fake change your gamecenter score get ihackcenter, it changes your client side score for you