Grrr turns out you can also do a POST request to the filter endpoint in Sugar.
Using POST works as it doesn’t attempt to translate the data in the post elements 
As an aside, putting the following into the url and ignoring the QS mapping will work for GET…
/<api version>/<module>/filter?filter[0][id][$in][]=id1&filter[0][id][$in][]=id2
My concern would be the url field may well have a character length limit so when built dynamically may well end up losing data, especially as sugar id’s are standard UUIDs.
Well, that’s a few hours down the drain, but at least I have a way forward with POST.
Thanks for all the communication guys, we got there in the end lol
Cheers
Simon