It seems to me that templates should not be lost when Asideshop is deactivated and then reactivated... instead I would request an option for "resetting" the Asideshop settings. It is common to deactivate plugins while troubleshooting and most plugins can be then reactivated without having to go through all the customizations again!
That plugin deletes the options on deactivation.
Until author changes that, you could try:
1. copying the plugin settings option_value before disabling (i.e. option_name of asideshop_options in the wp_options table)
2. after the upgrade
3. and after plugin reactivation
4. manually update that option_value you saved in step 1 back into that options record
Related
phpMyAdmin
Note: a previous enhance request by marecelolynch at http://wordpress.org/support/topic/172764?replies=26#post-762538
fncll,
Thanks for bringing this up. I will take this into account upon next release.