I'm currently planning a script which will update an additional field on our subscribers from an external database with around 200,000 entries but need to cross-check each.
Is there any limit on the no. requests we can push to the API during a period of time etc which is likely to pose a problem here?
The only limit in that sense is the one which will be imposed by network performance. 200,000 individual checks and updates will take a very long time. You can reduce that considerably by batching your subscribers. Rather than cross-checking them and then updating them each individually, you could consider getting a batch of 1000 active subscribers, cross check them all, and then update that whole batch in one call.
Apologies if i haven't correctly understood your use case, but if i have then going that will reduce the total number of calls and dramatically increase the speed of your update script.