This is maybe not a specific InDesign issue but it's the programme I use most so am starting here.
I am running CS5 on Windows 7. I have a constant problem that when I delete files in an explorer window they do not show as deleted. But if I refresh the view they disappear. Likewise if I am trying to rename a file I often get a message that the file is in use, even if I have closed the file. Closing InDesign solves it but I often get the problem even if it is not running. I am using an Intel RAID 1 system and an IT geek told me that using Windows RAID combined with Adobe software is what causes the problem. But he had no advice about how to fix it!!
It's not just an indd problem - same with pdfs, psd, ai. In the case of Acrobat I often get told the file is read only or in use - even if Acrobat is closed. But I'd be really grateful if someone on this forum has any knowledge of a solution.