1. When Update start it ask for Windows UAC username and password. How can I get rid from this.
Give wyUpdate full access to add, delete, change, etc. file in the target folder.
2. If I remove some files from user program folder's which I dont want to update like Configuration / Settings files. These files have settings values which are unique. The Update.exe remove file from destination / target folder. How can I avoid this problem
If you have a file in one version and the file is missing from the next version in wyBuild, then wyBuild sees that as meaning "delete that file". If you don't want wyBuild to touch a file then exclude it from all version and wyBuild will completely ignore it.