Encoding problem by name and file contents

Hi,

I would ask for an opinion to the most experienced.

After downloading files from a server (linux) to localhost, or when passing the same files from one computer to another, both with the same operating system (Windows 64 bit 8.1), I find myself very often (if not always) that individual files lost encoding in accented letters and special characters, this in all files, by the media, to .htaccess and config.php, to other theme’s php file, including the file .SQL database.

In the case of WordPress the .htaccess is tripled (rewritten here several times to understand).

For example, in the config.php file, we have everything written on a staff, not capabilities the reason but undermining their proper functioning.

For programming, as the development environment, using Xampp and NetBeans, NotePad ++.

May depend on an incorrect configuration of these programs? The Pc doesn’t have viruses and has not been modified in its operation at the operating system level.

To download and upload files using FileZilla, may depend on a bad config?

I repeat that all the programs I use are not normally installed on newly formatted Pc and no changes have been made.

Waiting your reply, thank you so much!