Missing Songs

Hello,

Continuing to try and work on the organization of my library and per your help from an earlier post, I have since moved all my songs to a single folder on my desktop and import to rekordbox solely from this location. All songs now in Rekordbox have the same file path and I've done this to mitigate duplicates, which up to this point has worked.  However, it came at the extremely costly time expense of having to re-sort thousands of songs back into Rekordbox created playlists and the loss of most of my cue points, etc. This has taken me months to re-do and is still a work in progress.  Currently, I've gotten through approximately 1500 of my 5600 songs - Ive still got a long way to go.

While working on this I've noticed that every time I close Rekordbox and re-open OR simply go back to Rekordbox (leaving the software open) to continue my work I'm getting the orange exclamation marks showing up beside tracks that weren't there before. To confirm my suspicions, I went back into a newly completed Rekordbox created playlist to discover a large number of orange exclamation marks beside recently sorted songs. When I sorted these tracks, I audio previewed each and every one so I know that at the time they were playable. When I try to 'relocate' the file and find the path (which is to my master music folder on my desktop) I get a message saying 'This file is already in your collection'. When I search through my collection by the individual track name, only the single (now missing) song with the orange exclamation mark shows up. What gives? How can I mitigate this new issue? 

I've gone to 'Display All Missing Files' and the number of files keeps climbing every time I check from about 500 to now upwards of over 750 songs.  I should add that not all of these songs are songs were newly sorted, a large number of them have yet to be sorted, therefore not all of the newly sorted playlists are missing in their entirety. When I started this new file path I checked 'Display All Missing Files' and every single file was accounted for, I had absolutely no orange exclamation marks. 

Please advise.