It looks like these two cases are different and not related to the same issue. Anyway, for both issues it is hard to suggest what could be the problem. Such issues require deep investigation. As I remember there was as similar issue (as pfellner described) in old Sitebuilder versions (I guess 4.0) and it was successfully corrected in future releases. I do not remember similar request since that time anymore. I guess ,this situation should be reported to Parallels support team for investigation. Before that, try to clarify with your clients if they did any special actions right before this issue appeared. There is always steps of actions which could reproduce situation, so if support team got it, they could provide all information to developers for further investigation.
As for E-shop issue, all shop items are stored in one database for the site which is stored on published side. So if some of items are there after migration rest of them should be also there. It also depends on how migration was performed. There is no build-in functionality in Sitebuilder for migration so I guess it was performed manually? But how?
Did you change publishing location for this site together with migration?
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