If I remember correctly we made the following change to htaccess..
Find:
RewriteRule ^([_0-9a-zA-Z-]+)/files/(.*) /wp-inst/wp-content/blogs/$1/files/$2 [L]
RewriteRule ^([_0-9a-zA-Z-]+)/wp-content/blogs/(.*)/files/(.*) /wp-inst/wp-content/blogs/$1/files/$3 [L]
Replace with:
RewriteRule ^([_0-9a-zA-Z-]*)/?files/(.*) /wp-inst/wp-content/blogs/$1/files/$2 [L]
RewriteRule ^([_0-9a-zA-Z-]*)/?wp-content/blogs/(.*)/files/(.*) /wp-inst/wp-content/blogs/$1/files/$3 [L]
Unfortunately I really didnt make any notes, so lesson learned, I will make detailed notes in the future!