Yes, I've seen this many times, usually with a database that has been converted up from version 6 or earlier. You can clean this up, but it's a bit of work. What you'll need to do is isolate down all instances of those external sources and change them to the single occurrence you want to use in these places:
1) Relationships graph
I find a tool such as BaseElements to be quite useful in cases like this; it will tell you where an external data source is being used, and when it's no longer in use.
I had a similar experience with a Filemaker DB I inherited. I was able to simply delete the extra versions of the repeated files in the File : Manage : External Data Sources window. I did verify that the files really were the same ones, and that there were no relationships, scripts, etc. somehow using those repeats.
Hoever, not knowing the exact details of your file setup, I do suggest either testing this out in a copy of the DB or making a backup of the DB prior to modifying the External Data Sources.
This usually happens with files that have been converted from an earlier version of FM (pre-7) when we did not have the control over file paths to external data sources that we have now. Old FileMaker used to create a new reference every time you added a file, especially if the file was moved around a lot.
So yes, you can consolidate these, but it will take a bit of work to do. You will have to find every file reference that uses the ones you don't want and change them to the correct one. The relationship graph is easy to do, just check them all and point them to the one file reference you are keeping. More challenging is script references - if you are running scripts from an external file, then the reference for that file has to be changed or you'll get the dreaded 'can't find the file" message. You have to change those one at a time.
If you don't already have the 2EmpowerFM Developer Toolbox - I highly recommend it. You can quickly search ALL your scripts for the file reference you are looking for and then change it. You can even choose "match case" to eliminate false results. Takes only a few minutes to fix and well worth the hours of time you will save with the many uses of this tool!
Yes it is a Pre 7 File. I am not going to consolidate that would take a long time. My concern is that I need to do this in every file.
For instance If I clean up one file, will that effect other files. Or am I required to clean them all up. I only need to touch one for now.
You can do each one individually. The changes only affect that file.
Again - with Developer Toolbox - you could probably do them all in less than an hour...