I am using Stellarium with EQMOD and wondered what the sync telescope command was in Stellarium?
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The telescope control from Stellarium is limited to reading the current telescope position, sending a selected set of coords to the telescope and a Goto command that will move the telescope to the selected coords. If this does not centre the telescope on the selected star the error will be in the telescope alignment and the correction (sync) will need to be made at the telescope.
There is another telescope control that can be used with EQMOD called Stellarium scope but it is not part of the Stellarium project.