@PamDenick
Ok, so I really appreciate everyone’s thoughts on this issue.
In summary, when trying to ascertain about a group of children I should ask Where are they? In Room 1? (for instance), but when I’m trying to distinguish that I’m looking for one child who has separated from the rest of the class I should ask but Where is he/she? He or she was asked to go to Room 2...
Language does not now differentiate between a singular child or a group of children, so unless we always use the child’s name (which might change on a regular basis) staff cannot distinguish if they are searching fo one child or many children.
it’s not easy to keep up.
In your example, where you're looking for a group of children, you would presumably give context - you wouldn't walk up to a teacher and say "Where are they?" and expect an answer, because they would quite reasonably have no idea what you were on about (and nor would they if you walked up to someone and asked "Where is she?" with no further context).
So either someone else says "I've been doing maths this morning with class 4" and you say, "Oh, where are they?". Or you say, "I'm looking for class 4, where are they?". Or you gesture at their usual classroom (or a sign saying 'class 4', or a class photo, or whatever) to indicate who you're talking about before saying "Where are they?".
As you necessarily need to have context when using pronouns - just as you wouldn't say to someone "She is dead" without giving them SOME clue who 'she' is - the "they" used in this scenario is therefore very clearly plural.
In the scenario where you're searching for an individual child, the same applies. Another teacher says "One of the kids in class 4 had a bit of a funny turn earlier and has gone for a sit down, just so you know"/"Someone from class 4 has gone missing"/"NeutralName from class 4 has gone to a different classroom".
Your response - "Oh, where are they now?"/"Bloody hell, where have they gone?"/"Which classroom are they in?" - is given context by the conversation around it, so it's perfectly clear that you're referring to an individual student.
Same with the example you use upthread:
Is Sam in Room 2? Sam was asked to go there straight after break. Where on earth is they?
The context ("Sam", one individual person's name), means that saying "Where are they?" is perfectly gramatically correct AND perfectly clear from context.
Using 'he or she' 'he slash she' in any of these contexts would be unusual and clunky. As PPs have said, singular they is widely used and - unless you've a tendency to start conversations halfway through and offer zero context - it's clear whether you're referring to a singular or plural they.