The SALES.QVW.SHARED is not important. It is created automatically by the QlikView server for every document that appears in the root folder, a mounted folder or any of their subdirectories.
IMHO the appearance of two Sales.qvw documents in the QMC tree (one in CamelCase and one in upper case) means that your deleted document was residing in a different location. Did you ever remove an entire subdirectory?
That's weird. If two documents in QMC - one existing, one deleted - have the same name, and they were residing in the same location (no mounted folder, no subdirectory etc.), I'm a bit at a loss here.
If you want to do away with this anomaly and recover the lost CALS, I suggest you run the Qlikview Server CAL Manager. It will help you in detecting lost CALs and how to recover them.
If you first want to figure out where exactly this lost document was placed and how to manually recover the lost CALs, you can configure your QVS to dump the .pgo files as XML also (restart required) and search the CalData.pgo.xml file which will contain all hidden details of the lost document. Instructions can be found here: Re: lost document cals