Relogix usually tries to preserve comments from the assembler source file (you can disable this, or limit the types of comment which are preserved, using a command-line option). However, because of the re-arrangement of the code flow, and the fact that several assembler lines may be combined together into one C statement, comments may be moved around, combined together, or removed altogether from the translated source.
In our example, the comments "Get token" and "Move into destination" are associated with the translation of the lines on which they were originally found. The comment "Hit end marker?" has been moved from the conditional branch instruction (which has been transformed into an if statement) to just before the if. The comment "Routine to move token block to buffer" has been moved into the function header.