Anyway, here's what I came up with. Might help someone else. The key take-aways are the "with selecting match" and "starting at top."
tell application "BBEdit"
set SearchStringOne to "{Script_One}\\n(.*)\\n{/Script_One}"
set ReplaceStringOne to "\\1"
--
set SearchStringTwo to "{Script_Two}\\n(.*)\\n{/Script_Two}"
set ReplaceStringTwo to "\\1"
set myDocument to document 1
tell myDocument
repeat 100 times
set myResult to find SearchStringOne options {search mode:grep, starting at top:true} with selecting match
if (found of result) then
set text of found object of myResult to grep substitution of ReplaceStringOne
tell script "UPPERCASE.scpt"
UPPERCASE(myDocument)— for demonstration purposes, this script turns text to all UPPERCASE
end tell
end if
--
set myResult to find SearchStringTwo options {search mode:grep, starting at top:true} with selecting match
if (found of result) then
set text of found object of myResult to grep substitution of ReplaceStringTwo
tell script "lowercase.scpt"
lowercase(myDocument)— for demonstration purposes, this script turns text to all lowercase.
end tell
end if
end repeat
end tell
end tell