If a file already exists on the site and you use FTP to upload another copy, it will retain the permissions on the original file and will not re-inherit the permissions from the folder. Windows considers this action to be a replacement and will use the same file-level permissions for the new copy.
This means that if you have custom file permissions set on an individual file that are different than the permissions on the parent folder, you do not need to reapply the permissions after every upload.
To force a file to lose any custom permissions, delete it, then upload a new version. Once the file is deleted, the next upload is treated as new file and will inherit permissions from the folder.
One other note: When using FTP, you may run into problems when uploading entire folders. Some FTP clients first delete the original folder, then re-upload an entire new folder of the same name. This causes any custom permissions to be lost and the replacement folders will inherit from the parent. If using custom permissions, its best to upload file-by-file to ensure they stay set.
If file permissions are lost, please contact Alentus via the Alentus Support Center and request that custom permissions on the file be reapplied. Enter this request by Submitting a Ticket to the Technical Support Department and be sure to include the URL, path, file name, and permission required.