When I import files into lightroom they come in dated folders. The majority of the folders only have a shot or two in them.
I have a folder with one item in it, I want to put it into another folder that has similar images in it (so similar in fact that the file names are 001, 002, 004, 005) the file I am trying to put into that folder is 003 but for some reason it will not go into that file. A message comes up saying that the file is already there when it isn't. How do I fix this? Is there an easier way to merge folders? I don't want folders and subfolders, I would only like to merge the images into one folder.
In my experience, when Lightroom says the file is already there, and the user says it is not there, I believe Lightroom. So this calls for further investigation.
But, if I were to suggest a solution, it would be different than the method you are trying to implement.
I want to put it into another folder that has similar images in it
Use keywords to group similar photos together. This not only has a whole lot of advantages over using folders (one example, a photo can have multiple keywords, while a photo can be in only one folder), but this eliminates the problem you are having of moving a photo from one folder to another, as there is no need to move photos now. And instead of searching folders for your photos, you have much more powerful tools in Lightroom to search by keywords and other metadata. Using keywords and other metadata really is a much better solution.
Moving the file is not necessary.
However, if you want to do so, and LR will not do it for you, use Finder or Explorer to move it, then in LR just tell it where you moved it to using the "find missing photo" process.