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If you delete all the subdirectories, you will have to delete all the songs from your library as well so you can have a clean import. The easiest way to do this is to go to Apps->MobileSheets->Clear Data, and delete those subdirectories (I'm adding a feature for the next update to clear the entire library in cases like this one).
The purpose of the feature was based around songs that use images. If you have 1000 songs that all used 5 image files, navigating through a directory with 5000 files is not fun. 1000 folders with 5 files each is much easier to manage.
By the way, if you don't want MobileSheets to make copies of your files, uncheck the Copy option and it will just use the files from their original location. Just be careful not to let MobileSheets delete any files when you delete songs (it's a checkbox option).
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Sorry, I think I misunderstood you a little. You must have other songs in your MobileSheets library, so deleting everything would not be good. You will have to manually delete all of the songs if you want everything to be cleaned up. The ability to multiselect on the tablet is going to be added at some point - sorry it's not already available.
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Sorry but I'm non the wiser. Let me recap in another way in order for us to converge.
1. I'm happy with the songs and setlists on my tablet. No changes required here.
2. My (originating) sheet music directory on my PC now has lots of subdirectories (created by Mobilesheets at import time) which I do not want. These subdirectories appear to have duplicated all the pdf files which were in my original directory.
3. Can I delete all the subdirectories on my PC without any adverse consequences (on either PC or tablet) when I next connect to the companion.
I hope this is clear.
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In response to 2.), MobileSheets should not be creating any directories on your PC. Did you mean tablet? It sounds like you now realize you need to disable the copy options. Are your songs pointing to the files in the subdirectories? If so, you can not delete those subdirectories without the songs failing to load. You will need to edit each song and fix the file (or use the swap pdf feature), or delete the songs and recreate them. If your songs are using files from the location you want, then you can delete those subdirectories without any consequences.
Mike
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You can edit a song, then press and hold on a file, then tap "View Full Path" to see the full path on your SD card to where the file is stored.
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That is a correct statement. Delete away.