Hello @Lukasz Czerwinski
you can specify list content permission for the folder
and for the specific file you set permission as Edit
you description is little bit contreversery , saving a file in a specific location is mean that you have by default modify permission in that file then depending in what location "folder" that you have access or not.
Maybe if you can specify more the need or the user cas you have so we can provide rafine solution
Thank you
Mustapha