Files Version Control

I'm trying to accomplish this:
https://github.com/h5bp/html5-boilerplate/wiki/cachebusting

But if FURLS are enabled these two sets of rules conflict with each other.

# Enabling FURLs
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?q=$1 [L,QSA,NC]

# Version Control
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.+)\.(\d+)\.(js|css|png|jpg|gif)$ $1.$3 [L]


I wonder if there's any way to friendly merge them.

If merging wasn't an option any other suggestions for this issue? My only guess is creating (static) resources or chunks for css and js files.

Thanks in advance!