bypassing the 5000 records read limit

We have different users doing different read process on objects that should result in more then 5000 records being read. It is impossible to start creating and extra column for every businessprocess on every object to filter out the records already processed. Is there a way get the next 5000 records, without having to update a dedicated flag for that business proces? Some of those business processes should run simultaneously, so in that case a dedicated flag to trace the already processed records doesn't work.  Is there another way to bypass that?