To make the huge bubble not flip it's lower half of the graphics vertically, you need to edit the adress $02E382 (the place where the game has the bubble's graphical properties) and change the eight $BB's listed in it into $3B. The easiest way to do so is by making an asm patch that lets you change the values manually, kinda like this:
org $02E382 ;Loads the properties of the Green Bubble
db $3B,$3B,$3B,$3B,$3B,$3B,$3B,$3B ;Properties of the upper half of the bubble
db $3B,$3B,$3B,$3B,$3B,$3B,$3B,$3B ;Properties of the the lower half of the bubble.
;Value was changed from $BB so it no
;longer flips vertically
You can copy paste the code into a notepad and save the file with the .asm extension so it becomes a proper patch. Then you grab ASAR, use it to patch it and voila. The bubble no longer flips it's graphics for the lower half.
Now, if you also wanna force the thing to use use the whole 64x64 square where the Big Boo graphics are, then you could also add this bit to the patch below the initial code:
org $02E372 ;Tilemap of the Green Bubble
db $80,$82,$84,$86,$A0,$A2,$A4,$A6 ;Tiles used by the upper half of the bubble
db $C0,$C2,$C4,$C6,$E0,$E2,$E4,$E6 ;Tiles used by the lower half of the bubble.
;Values have been changed so it loads
;the lower half of the Big Boo GFXs.
Do note that you no longer will be able to use both the bubble and the big boos on the same room due to the graphics overlapping, but even then, you can always relocate the bubble's graphics to somewhere else if you so wish.