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I used to see inconsistent behaviour with deleting files as well a few weeks ago (on gigabeat F, but for this problem that shouldn't make a difference). When I update to the latest build to do detailed tests the problems were gone, so i suspect that upgrading will also help for you
version r17202-080421Another maybe related issue, if you delete a file while playing it, it continues to play. However, RockBox may hang at some point 10-20 minutes later while still playing the same file.
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