Most likely you are missing the QSA
flag: "query string append":
RewriteEngine On
RewriteRule ^(.*)-filter-(.*)\.html$ $1.php?filter=$2 [QSA]
RewriteRule ^(.*)\.html$ $1.php [QSA]
I suggest you take a look at the excellent documentation of apaches rewriting module. It explains such things in detail and has lots of really good examples.