I will remove all files in folder logs and manager/logs.
Does it have any effect to my streaming VOD ?
No, wowza should create new files to continue logging. In some cases, such as when using SELinux, wowza may be unable to automatically create new files, but streaming itself should continue to function normally either way.
It may be better to move files to a temp folder first, instead of deleting them immediately. Just check if new log files will be created.