negative logic: ( a & b) <=> (!a | !b)

you want to select

WHERE a OR (b AND NOT (c AND d))

which would be equiv. to

WHERE a OR (b AND (NOT c OR NOT d))

so either:

(@IncludeUnavailableBookings = 'Y') OR

(@IncludeUnavailableBookings = 'N' AND NOT (A.Col1 = 'X' AND A.Col2 = '-99'))

or:

(@IncludeUnavailableBookings = 'Y') OR

(@IncludeUnavailableBookings = 'N' AND (A.Col1 <> 'X' OR A.Col2 <> '-99'))