set exist=##class(%Dictionary.CompiledClass).%ExistsId(ClassName)

will tell you the status

If there is an index defined on PBD_PBO_ParRef  is it correctly generated?
If not sure, do rebuild index from MgmtPortal. 

What about chopping your query like this or similar

lastID=0

"Select TOP 10000 ID,Text from eprinstance.isegment where ID > ?"

passing lastID as query Parameter

Now you loop on it until you collected all records.

The basic idea is to limit your result set by TOP as your partition allows.

it's definitely independent of Cache versions.