Bootstrap reloading of webfiles removes some existing files

During a new deploy some webfiles are not displayed on the site. I have to manually upload all files and then restart each sites.
In my project the files are:

• FontAwesome.otf
• fontawesome-webfont.eot
• fontawesome-webfont.svg
• fontawesome-webfont.ttf
• fontawesome-webfont.woff
• fontawesome-webfont.woff2
• favicon.ico