Reply from Seean O'Connor (thanks Seean) quoted below:

On Thu, Jan 12, 2012 at 6:11 PM, Seean O'Connor <capricorn8159@gmail.com> wrote:
as a user of Fl studio( and lmms) I can confirm that Fl does have the same limitation whereby file consistency has to be maintained in order for the sound/sample in your project to remain intact when migrating projects .( although has a workaround in which the whole projet plus associated samples and patches can be saved as a compressed file that, if i am not mistaken preserving the links between projects and associated sound/patch files when migrating to another system

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