What's the difference between them?
I am interested in a generic definition, but here is the sentence I was writing:
"The file is located at/in the images folder."
in would refer to a container holding the object.
The pen lies in the box
at would refer to the location of the object.
The box is at the shop
In your context, as the folder contains the file, therefore, use of in would be appropriate.
Of course, they, at times, can be used interchangeably (Thanks @FumbleFingers). This link gives a nice comparison between the use of at and in.
Well, I will go with
located in the folder here, which sounds more natural. Files are generally stored within the folder of a computer system, so the proposition
in is more appropriate and accurate than
at. the proposition
at usually go with home/office/university/point/stage/time/... these words and so on, indicating where/when exactly things happen.
"Located at" is wrong, and "located in" is not wrong, but I'm reluctant to call it correct because I find "The file is in the images folder" preferable to "The file is located in the images folder." Also, if you are writing documentation (vs. speaking conversationally) write "File x is in the images folder"; that is, name a specific file in the sentence instead of depending on context or a previous reference.