I'm sorry to say that there is nothing we can do about it at the moment.
The number of revisions per item is limited to 5000, and we have no way of removing old revisions yet.
The limit exists to ensure that automated synchronisations don't go crazy and fill our database with revisions.
I've filed an internal product input to rotate revisions, so that when number 5001 comes in, number 1 goes out, etc etc.
In the meantime the only thing I can suggest you is to clone the item (e.g. PodioItem::Duplicate) and update items via the API as a result of an actual change, not via automated time interval.
The cloned item will not have the inbound relationships of it's original, but will have the correct outbound relationships (if any).
Hope this helps.