Most likely, there is a caching issue with the simulator's plugins, on your side. To check if this is indeed the case and to fix it, please delete the AppBuilder Cache
folder. You will find it under %localappdata%\Telerik\BlackDragon\.
After this, you should notice a slower initialization of the simulator, as it will download the plugins sources, again.
I hope this solves the matter. If it doesn't however, please contact us again with some additional information, like which AppBuilder client is being used for your development needs, or how exactly you use the SQLite plugin.