Here's a
rough script (
not fully tested) that might be handy. Place this script in your .../AutoHotkey/Compiler/ directory. Place your altered .bin files in the /binfiles/ directory that gets created when the script is run for the first time. Feel free to tweak it

.
Code:
; Generated using SmartGUI Creator 3.4
IfNotExist, %A_ScriptDir%\AutoHotkeySC.bin
{
MsgBox, Please copy this script to your .../AutoHotkey/Compiler/ directory and run the script again
ExitApp
}
Gui, Add, GroupBox, x6 y20 w570 h90, Required Parameters
Gui, Add, Text, x16 y50 w90 h20, &Source (script file)
Gui, Add, Edit, x136 y45 w315 h23 vSource, ; Source Edit1
Gui, Add, Button, x458 y45 w53 h23 gBsource, &Browse
Gui, Add, Text, x16 y79 w99 h13, &Destination (.exe file)
Gui, Add, Edit, x136 y75 w315 h23 vDest, ; Destination Edit2
Gui, Add, Button, x458 y75 w53 h23 gBdest, B&rowse
Gui, Add, GroupBox, x6 y120 w570 h180, Optional Parameters
Gui, Add, Text, x16 y184 w102 h13, Custom Icon (.ico file)
Gui, Add, Edit, x137 y180 w315 h23 vIcon, ; Icon Edit3
Gui, Add, Button, x460 y180 w53 h23 gIcon, Br&owse
Gui, Add, Button, x518 y180 w53 h23 gDefIcon, D&efault
Gui, Add, Text, x16 y225 w57 h13, &Passphrase
Gui, Add, Edit, x137 y220 w315 h23 +Password vPass1, ; Pass1 Edit4
Gui, Add, Text, x17 y249 w114 h13, &Verify passphrase
Gui, Add, Edit, x137 y246 w315 h23 +Password vPass2, ; Pass2 Edit5
Gui, Add, Button, x460 y232 w53 h23 gDefPass, Def&ault
Gui, Add, Text, x25 y271 w467 h16, Note: If a passphrase is specfied`, you will need it if you wish to "decompile" a script.
Gui, Add, Button, x264 y314 w75 h28 gConvert, > &Convert <
Gui, Add, Text, x16 y155 w102 h13, Custom .bin file
Gui, Add, Edit, x136 y150 w315 h23 vBinFile, %A_ScriptDir%\binfiles\AutoHotkeySC.bin ; Edit6
Gui, Add, Button, x459 y150 w53 h23 gBbin, Bro&wse
Gui, Add, Button, x518 y150 w53 h23 gDefBin, Defa&ult
IfNotExist, %A_ScriptDir%\binfiles
{
FileCreateDir, %A_ScriptDir%\binfiles
FileCopy, %A_ScriptDir%\AutoHotkeySC.bin, %A_ScriptDir%\binfiles\AutoHotkeySC.bin
}
IniRead, OutputVar, %A_ScriptDir%\a2egui.ini, AHK, Version
If OutputVar <> %A_AhkVersion%
{
IniWrite, %A_AhkVersion%, %A_ScriptDir%\a2egui.ini, AHK, Version
FileCopy, %A_ScriptDir%\AutoHotkeySC.bin, %A_ScriptDir%\binfiles\AutoHotkeySC.bin, 1
}
Gui, Show, h356 w586, AHK2EXE Gui - c1
Return
Bsource:
GuiControl, Text, Edit1, % Browse1("3", "*.ahk"," ")
Return
Bdest:
GuiControl, Text, Edit2, % Browse1("S3", "*.exe"," ")
Return
Bbin:
IfNotExist, %A_ScriptDir%\binfiles
{
FileCreateDir, %A_ScriptDir%\binfiles
FileCopy, %A_ScriptDir%\AutoHotkeySC.bin, %A_ScriptDir%\binfiles\AutoHotkeySC.bin
}
GuiControl, Text, Edit6, % Browse1("3", "*.bin", A_ScriptDir "\binfiles")
Return
Icon:
Icon := Browse1("3", "*.ico", A_ScriptDir)
If Icon
GuiControl, Text, Edit3, %Icon%
Return
DefBin:
GuiControl, Text, Edit6, %A_ScriptDir%\binfiles\AutoHotkeySC.bin
Return
DefIcon:
GuiControl, Text, Edit3,
Return
DefPass:
GuiControl, Text, Edit4,
GuiControl, Text, Edit5,
Return
Convert:
Gui, Submit, NoHide
If BinFile =
BinFile = %A_ScriptDir%\binfiles\AutoHotkeySC.bin
FileCopy, %BinFile%, %A_ScriptDir%\AutoHotkeySC.bin, 1
IfNotExist, %source%
{
MsgBox, Please specify a valid source file
Exit
}
source := "/in " SFN(source)
If dest =
{
MsgBox, Please select destination
Exit
}
IfExist, %dest%
MsgBox, 4, , File Exists. Overwrite?
IfMsgBox, No
Return
dest := "/out " SFN(dest)
If Icon
Icon := "/icon " SFN(Icon)
If Pass1
If Pass1 = %Pass2%
Pass1 = /pass %Pass1%
else
{
MsgBox, Password verification failed
Exit
}
RunWait, %A_ScriptDir%\ahk2exe.exe %source% %dest% %icon% %Pass1%
FileCopy, %A_ScriptDir%\binfiles\AutoHotkeySC.bin, %A_ScriptDir%\AutoHotkeySC.bin, 1
MsgBox, Compile complete
Return
Browse1(options, filter, path="")
{
FileSelectFile, OutputVar, %options%, %path%,, %filter%
if OutputVar
Return, %OutputVar%
Return
}
SFN(fname)
{
Loop, %fname%
{
if A_LoopFileShortPath <>
fname = %A_LoopFileShortPath%
}
Return, %fname%
}
GuiClose:
ExitApp
; Ahk2Exe.exe /in infile.ahk [/out outfile.exe] [/icon iconfile.ico] [/pass password]