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On the Linux version of Scrivener the conflicted versions of the *.scriv files in the project folder may prevent Scrivener from opening that file. The only indication of an issue is in the Terminal (a good bet for debugging Linux GUI apps is to launch them from the Terminal).
The problem is easily fixed by removing the extraneous .scriv files - just make sure you keep the most recent version.
Prevention is as simple as not having the same Scrivener project open on two computers at the same time.