Mistaken scope of a command command wiped out a file

I have been happily running NLPro without a problem except for difficulties working out after finishing a conversion when a command works on a single image or the whole collection I have just converted. I made the same error wanting to remove a bad image and erased off the disk a whole film. It was impossible to undo this command.and thinking that this segment would have to be reloaded into lightroom I therefore copied the whole file into the lightroom folder and imported them Lightroom complained that there was not enough space to load two images even thought I have a terabyte of available space. However when developing all over again with NLPro I find that I now have duplicate files throughout this folder. I had assumed that lightroom would refuse to import duplicates, and I do not know how I was able to load duplicates into the file that provides the basis for the lightroom catalogue, I think it would be a good Idea to warn people of the scope of their commands when they have completed a NLPro conversion. I also wonder whether this has somehow fouled up lightroom as whole file was somehow disrupted.*