My setup: I have several projects in the previous version’s format and I sync them between different machines using a web storage service. I open them via shortcuts that point to .scrivx files. Web sync sometimes temporarily fails, with the result that the .scrivx file is missing for a few seconds. I understand and accept that behaviour.
What happened: I tried to open and convert a project in the old format. Scrivener opened and converted a different project. Specifically, the last one that I had worked on during the previous session. I was later able to open and convert the project I wanted to.
My reconstruction of events: the web sync had failed for the project I tried to open. Scrivener tried to open the project that the link pointed to, but the .scrivx file did not exist or was unreadable. Scriener failed over to opening the last project in the MRU list.
Sugestion: when Scrivener fails to open a project given on the command line or a link, it should issue a warning before opening another project.