In , 'backup' functions as an adjective or substantive noun, and it refers to a file, a backup file.
 Please note that [the] original index.html file was [a] backup [file] and [it was] renamed as 'index.html.bak'
Note, html isn't a backup file, so  is the meaning you're looking for:
 Please note that [the] original index.html file was backed-up and [was] renamed as 'index.html.bak'
In , 'backed-up' functions as part of the verb phrase 'was backed-up and [was] renamed'. I believe  is the meaning you're after. Note, the original index.html file was backed-up and then renamed as index.html.bak, which is a backup file.
- For Teachers