Let's say I have 50 GiB of files that weights around 500 KiB each.

My guess is that having, for example, 5 large files of 10 GiB each with the same content archived in them would be better for hard drive performance. Am I correct?

Will there be a noticeable gain on an NTFS filesystem?

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Finally, which tool could I use to group the files together while retaining the ability to modify the content of the archive with zero or minor performance loss? For example, I like TrueCrypt archiving because after mounting an archive file, it creates a drive which I can use seamlessly as if it was a normal drive. The only thing with TrueCrypt is that I don't need encryption/compression, only archiving.