Sed remove end of line for specific lines

awk '
    {
        if (/^□ /) {
            if (prev_line) 
                print prev_line
            prev_line = substr($0, 3)
        } else {
            prev_line = prev_line " " $0
        }
    }    
    END {print prev_line}
' raw.txt

I have box and space in front
I am a large line which will get appended to next line.
I am another line.

You can use getline in your awk to fetch the next line:

awk '/^>/{ if(!seen[$0]++){ print;getline;print } else { getline } }'

There is a simpler answer that also handles multiple lines:

awk '/^>/{ skip = seen[$0]++ }
     { if(!skip)print }'