Making comparisons across LR folders

Other than by assigning individual photos flags/colors/ratings and then filtering within each of two folders, is there a way to have all the files in two folders show in library view simultaneously, and then select a photo from each to compare? And then quickly switch to another whole folder to make the same comparisons with one of the original two folders?

I am not sure what you are really trying to accomplish but it sounds like you are looking at possible duplicates and trying to select the best image? Whether you have your images located in a single folder or folders using a date or location or even the month and moon phase, LR sees your images as a dynamic collection of images that you define using folders, quick collections, defined collections and/or selections based on keywords, color labels, file attributes or just selecting a group of images with your mouse. The end result is a set of photos that you can manipulate.
Where this gets tricky is that when you do use folders and you select one on them, that selection becomes the ad hoc collection that LR will display. If you select a different folder, you get a new collection of photos. You can't select more than one specific folder at a time. You either have to select a folder higher up in the hierarchy that contains all of the folders you want to look at or build your own ad hoc collection of images that does not depend on specific folders. Based on what I perceive you are trying to do, I agree with JimHess. I would create a quick collection that includes all of the photos I am interested in viewing together. In your case, the two folders you want to compare as well as the third.
As for differences between the two methods, using ratings, flags and such has two potential issues. First, it is possible that not all images in the specific folders you are interested in will all contain your chosen search criteria and second, it is just as likely that photos outside the specific folders you are interested in will also have them. Either way, you may not get exactly what you are looking for unless you specifically set up the search to look for something that you are certain only the photos you want to look at all have that criteria associated with them.

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