I have 2 files with jquery code in custom directory www.mysite.com/files/js/...Every time I clear cache, the files are deleted from server. How is this possible? Anyone came across this issue?
Files were added using drupal_add_js inside node body using php filter. Path was 'files/js/myfile.js' without using domain name. I resolved it by changing directory name from 'js' to 'js-custom'. I think 'js' directory was created by some module there and was emptied after each cache flush. Now everything works ok.