Library is a mess after creating a second library

I have my library on a external hard drive, 4600 albums. No issues, every album with artwork, no duplicates just aa clean library organized how i like it. No compilations, no various artists as a album artists name. I had a bunch of music on an old ipod sitting on my desktop so i decided to organize it via a second library. big mistake. The net day I opened up itunes for my original library and its a complete mess thousands of duplicates and missing songs, and its all in the cloud i have itunes match. Even tho I see my files in their original place on my external drive itunes does not recognize that they are there. If I download a album I get 2 of everything in itunes and in windows explorer ie the external hard drive. I looked around the external hard drive for the itl. file but the newest file i found is 5 weeks old and ive been using itunes every other day from that old file itl. date. I confused as why is there not a more current itl. file like when the last day I used it a couple days ago as apposed to the dated file 5 weeks ago. How can i get my old library back? How do I save my library after I use itunes or do any work to my library? sometimes I will rip some cd's and i will get the itunes library error could not be saved due to not enough space and i will have re rip the cd's again. there is enough space on external drive and internal drive for that matter. I would like to save my work ] library whenever I make changes or when needed?