Hi,
Which BW version are you on ?
If it is 7.3, major enhancements have been done to ensure consistency of transport requests at the release action.
So, yes gathering a lot of queries in the same transport can be hard to debug, but, even 20 queries in the same transport request can be a nightmare...That's why, I would go for a first try with all the queries to a sand box and after that, I will debug
By the way, are you using the standard transport process or the Bw one ? If you use the standard transports, when you will delete the queries from the query designer, you will be prompted a popup to use or create a transport request. Then, all the necessary objects will be collected as if you were changing something in the query...so it should be OK!
PY