As we know, a large chunk of the 84 cast were taken offline by the mindwashed Optimus Prime in Prime Time!. However, in the UK continuity, they along with most other 84 cars were kept alive and continued appearing. But by Funeral for a Friend!, both Prowl and Ironhide are shown to be offline (Or at least badly injured), despite both appearing just issues ago. This is of course due to Friend being a US publication. So apart from that obvious explanation, what do you think happened to them between Resurrection! (Their last appearance) and Funeral for a Friend!? Considering the Combaticons are introduced without much fanfare in the issue following Ressurection!, could Megatron have taken them on a test run that resulted in Prowl and Ironhide (Along with possibly others) being badly damaged, prompting the Protectobots' construction to be sped up?
I found this on TFwiki's page for "Funeral for a friend!" "In the US continuity, Prowl has been damaged since "Prime Time!". In the UK continuity he recovered and was seen last attending (fake) Optimus' funeral in "Resurrection!". What caused the injuries seen in this episode for the UK continuity is never mentioned." Perhaps the same could be said for Ironhide? Or maybe I missed something, perhaps look on the respective pages on Tfwiki and perhaps you can find something?
That wiki page is incorrect. Prowl is seen in the US issues #14 and #16, both of which are after Prime Time. As to the original question, they were clearly injured in an off panel adventure. It's reasonable to assume there are plenty of skirmishes between the two sides we don't see. Combaticons are as good as any, I like that.
It's Bluestreak who appears functional in #14 (he's miscoloured like Prowl, but you can tell it's him by the shoulder cannons). Prowl is visible (badly drawn) laid up in the repair bay scene the same issue, the same as all the other Autobots who were damaged in the fight in #12. It IS Prowl in #16, but that's a fill-in issue that has some other characters in places they're not supposed to be, and coloured wrong while they're at it (Laserbeak and Buzzsaw) and given that the only other Autobots of the small number who appear in the story are ones who, continuity-wise, are meant to be active at that point, it's a pretty clear goof and should've been Bluestreak too.