Not sure whether this is a bug or a works-as-designed but I've just noticed this with FME 2016.1
I have started with an empty workspace and added 2 Shapefile readers, which I renamed to "OLD" and "NEW" (setting up a simple ChangeDetector demo). I then realised I made a mistake, so I deleted both readers and re-added them. However, on re-adding them, even though they were pointing to different shapefiles as before, the names were automatically set to "OLD" and "NEW".
It keeps happening, so if I delete NEW and add another Shape reader it'll be named NEW. If I add a reader for another format it'll get a default name, if I then add another Shape reader it's again named NEW. It kinda looks like the 1st Shape reader in this workspace will be called OLD and the 2nd one NEW.
Right now that's totally fine with me for what I want with this demo, but I'm just wondering whether this is how FME is designed to work :)