Im using http://mw.modhistory.com/download-68-10001 which allows you to brew poisons. There's a specifix messagebox I cant remove -

if ( onActivate )
if ( pAlcSkill < 30 )
messagebox "This object requires 30 Alchemy skill to use."
set pickMeUp to 1
return
else
set opened to 1
Activate
messagebox "Silence = Calm, Lock = Soultrap" ; just a reminder for player
endif
endif

if ( opened != -1 )

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The one in bold.

If I try in the CS the mod will not save properly, and if I try in MWedit, the mod wont work properly when I load it up. I know you shouldnt edit scripts too much but Ive removed dozens of other mods messageboxes and had no problems at all.

If there's a reason why it can't be removed, perhaps make it impossible to execute by wrapping it in "if 0 ... endif"? Then any reference to the message is still there, but you can't ever see it.

Make sure the "customfunctions.dat" file found in your MWEdit folder is up to date. You can get the latest version on the MWSE download https://github.com/Merzasphor/MWSE/releases/.