After Rebuild vHosts all settings in /usr/local/apache/conf.d will resetted

Hi,
I change some Options in the ssl.conf because there are still RC4 and some old options. Everthing is fine until I Rebuild the Apache Vhosts from the CWP-Admin-Backend. After the rebuild Apache vHosts all the modifications in  the conf.d folder are resettet relaces (I also hat try to delete the ssl.conf file and setup a new one with a different name, but after rebuild the Vhosts all deleteted files are back, apche is broken cause of configuration conflicts tow times Listen 443 and so on).
Is this normal? Were can I change the "globale-configuration" to make itstill active/available after use the "Rebuild Apache vHosts" function?

Location for my changes: /usr/local/apache/conf.d/ssl.conf
OS: Centos 7 64Bit
CWP: CWPpro version: 0.9.8.539

Is this normalen? A bug?

Found anything on that?

rebuild checks for missing files and adds them, if you made some custom then this could be bad as you should modify existing