This can happen if a graphic in the artwork contains the swatch. This means that it's not an indesign swatch - but an imported swatch used by a graphic.
Why delete it? InDesign will only output what's used in the file. So if you go to the Ink Manager you can choose the option to convert all spot colours to CMYK and make sure to tick use LAB values.
If this isn't the case - there could be minor corruption in your file - you can use File>Save As and choose the IDML format (also can be done by going to File>Export and choose IDML - it's the same thing).
Open the IDML file and it opens as Untitled.
See if you can delete the swatch now.
If the swatch still cannot be deleted - then you can do the following.
Change the Extension of the IDML to .zip.
Unzip the file - IDML files are just glorified zip files.
Go to the Resources file once unzipped.
Open the Graphics.xml in a text editor like Notead or Text WRangler
Search for the name of the swatch.
There should be text after this that says "Color Removable="false""
Change this to true.
Save and exit the file.
Rename the original file back to .idml
OPen in InDesign - and then you should be able to delete the swatch.
Thanks for all the options. I think the file might of been corrupt.