Have you tried to open the Scene file?
I am betting, you can do one of the other.
1: catch that sprite in the scene editor file, (outside AGKS, just in notepad , i Use NotePad+ as it is awesome and free) find it, delete its line but do not forget to find it also at the Delete Scene function.
2: you can copy the entire scene file to another scene file created in AGKS using the same method. Create a new scene IN AGKS and close AGKS. now open NotePad+ and open both files. copy paste everything just without that single sprite.
You can use NotePad+ to also find that sprite position and change its X or Y or both.. which is another option.
Also, on the left panel in AGKS it writes all your Sprites \ Texts and stuff so you can select it from there and change the X on the right properties panel, then delete it.
about renaming the other sprite. you can always just rename the sprite and inside your code search and replace all found items. Ctrl + H.
I also had some problems with an "Editbox" i have inserted in a Scene file and deleted it but for some reason which i have no idea why.. it wasn't deleted in the Delete Function in the Scene file, opened notepad+ and deleted that line and everything worked out, on another hand i just created a new scene file.