1) Select and copy a carriage return in the BBEdit document.
2) Perform a Find (Search > Find...), and paste in the return in the top (Search for) field.
3) Type a Tab in the bottom (Replace with) field.
4) Hit "Replace All"
If that doesn't work, type \r in the top field and \t in the bottom field. Those are the symbols for carriage return and tab respectively.
Make sure the cursor is at the top of the document when doing a find and replace, otherwise it'll just look after the cursor.