After a fun five hours on this, I am no closer to working out the underlying problem, so I have emailed eSellerate for some insight into the matter. I have a feeling it is to do with the older eSellerate engine that Scrivener 2 uses, but I cannot understand how the two serial numbers would interfere with one another.
I do have a solution for you, though:
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Download Scrivener 2.9 (follow the “Download an Older Version” link on our Downloads page). If you’ve already downloaded it, re-download, because I’ve made an edit to the code that will make deactivation easier.
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Replace your existing version of Scrivener 2 with Scrivener 2.9.
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Launch Scrivener 2.9.
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Go to Scrivener > Registration… and deactivate your licence. Don’t worry if you see a deactivation error. I’ve made it so that it will remove your serial number details anyway.
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Quit and relaunch Scrivener 2.9. (This part shouldn’t be necessary, but it sometimes helps avoid activation issues.)
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Go to Scrivener > Registration… and enter your Scrivener 3 user name and serial number.
Scrivener 2.9 can be activated with a Scrivener 3 serial number, and doing this avoids whatever problems are going on with trying to run concurrent activations of two versions, because now the activation is the same for both.
I’ve tested this a few times and it has solved the issue for me, but let me know how it goes.
All the best,
Keith