Jean-Baptiste Lallement had an interesting solution.
To not close the close the running synaptic but reuse it instead for reloading.
** This bug is no longer a duplicate of bug 52630
Retry option for database lock situations
** Changed in: synaptic (Ubuntu)
Importance: Undecided => Low
** Changed in: synaptic (Ubuntu)
Status: New => Triaged
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Reload Package prompt gives up when another Synaptic is running
https://bugs.launchpad.net/bugs/529847
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