I’ve made a mistake on editing our website template which led to analytics being tracked for another website id (which was “dead” for that time - no data had to be collected for it).
I was able to fix the idsite field in tables piwik_log_visit and piwik_log_link_visit_action since I found the date since that the error was online and recreated the achives.
is there any way to reconstruct the goals for the missing part of the timeline (from raw log data in the two tables I mentioned)?
There is no way to reprocess goals at this stage (even though it could technically be done with few hours work). You can look into http://piwik.org/consulting/ if you wish to have this feature!
There is a plan because there is a ticket, but it is not scheduled yet. If anyone can sponsor this change (or others) get in touch with consultants: http://piwik.org/consulting/