I imported photos. In many folders only some pictures show up in LR library. Pictures are still in original folder in hard drive as shown by Windows Explorer but not in LR library folder. Worse, when I find them in another file and try to copy them to the LR folder, LR won't copy because it says they are already there.
You have most likely imported the photos (accidentally?) using the COPY option, so Lightroom is accessing the copy in a different folder.
DO NOT IMPORT BY ALLOWING LIGHTROOM TO IMPORT DUPLICATES!
If you haven't done any work on these photos yet (like editing or adding metadata), you can just delete them from Lightroom and then import them with the ADD option. If you have done work on these photos, then DO NOT DELETE AND IMPORT. In Lightroom, I believe you would want to right-click on the folder that Lightroom thinks the photos are in and select Update Folder Location and then select the desired folder.