I'm not familiar with what might be available with Angel's and Bob's, but this is what comes to mind from vanilla.
The laborious but complete option would be to do a rolling shutdown of your logistics network: starting from one edge, remove roboports, and then put them back but making sure the old network and the new network never touch, and the new network contains no old robots.
Assuming you don't want to do that:
(As Vyndicu's answer already mentioned, but for completeness:) For any given roboport, you can use filter inserters to extract specific types of robots. This can be used to collect the stragglers automatically in the long run, but requires you to make a change at every roboport whenever you get a new upgrade.
You can encourage robots to stop in particular roboports by creating a very large jobs which will be finished in the vicinity. The best procedure I have thought of is:
- Set up inserters to extract robots from the area(s) where you keep your storage chests, and an unused area nearby.
- In the unused area, make many requester chests with large requests of something you have stockpiled (e.g. stone or coal you mined before building on top of the deposit). Your logistic robots will do this job, and then park themselves in the nearest roboports.
- Order deconstruction of those requester chests. Your construction robots will do this job, and then park themselves in the nearest roboports.