I have used Vera elsewhere and transitioned quite a similar large setup from Indigo a few years ago. My advice would be to migrate one ‘piece’ at a time, keeping both systems running in parallel at least to start with.
Also, the advanced flows in Homey are extremely flexible (for me this is the killer feature of Homey vs any other system). So rather than recreating every piece of logic implemented in the exact same way as you have elsewhere, you should be able to condense down to a much smaller number of flows overall. Bear in mind you can have multiple separate flows each with their own trigger cards all within one advanced flow so that you can keep all the logic related to one sub system in your automation together.
Finally, think about how to organise and name your devices and flows in Homey from the start. Take a look here for some thoughts on organising flows [HOW TO] Alternative approach to structure and organise your flows
