The regular form
- War er ... 'was he ...'
would, in certain positions of sentence in my idiomatic sociolect, sound approximately as
- * wara /vaːʁɐ/.
I can not imagine at the moment how this came about. It looks like metathesis, because war /vaːɐ̯/ alone elides r to a schwa, and, in any event, the final vowel of /vaːʁɐ/ should belong with the enclitic. Does the schwa alone account for Er /eːɐ̯/, as suggested by wiktionary 1 (eg. was er 'what he' /ˈvas‿ɐ/ not exactly identical to Wasser 'water' /ˈvasɐ/ eg. because of tone contour)?
Logically, then, war er would become /vaːɐ̯‿ɐ/? I don't think war is subject to liason; it might be useful to posit a glottal stop instead, but its phonemic status is chiefly denied. Hence it seems reasonable expecting that the /ʁ/ belonged with the clitic, and I would transcribe perhaps /vaː'ʁɐ/ or /vaʁ:ɐ/ but I have no command of a phonology lab to affirm this. Rather, as so often, I suspect a deeper relation.
For one, the verb war 'was' < *was is said to have been leveled on the model of plural waren, subj. wäre 'were' < *wez- in older stages, where the voice and subsequent rhotacism is regular if I understand correctly.2, 3 So, there would be a slight difference if indeed my * wara appears dominantly at the start of questions in a kind of subjunctive mood, cp. eg. 3rdP.sg.subj *wēzī > ModHG wäre er, wär'er with umlaut due to influence of the former high vowel. It's not clear when umlautung began. It cements itself in Middle High German. Thus it might be possible that I have inherited two different reflexes of the same root through two different branches; the regiolect here is close to German Low German and, the metrolect is however a mixed bag, nominally High German.
That said, how is this relevant to linguistics? It simply isn't, if my last sentence is correct. Aothough, (i) if the ending is not from the German subjunctive but something more particular, or (ii) if this is a reflex of PIE *ey non *iz, q.v.4, or (iii) not either but both, or something entirely different, (iv) then it might fall outside the scope of modern German philology and within the field of pre-historical linguistics. A cognate phrasal verbiage outside German would suffice to reach conviction in the simplest case (BrE * wuz'e for a start, or even ye, cp. Ger. 2ndP.pl and honorific 2ndP ihr /iːɐ̯/, as "er" can be found in the second person as well, though late, with limited use and drifting connotation, formerly honorific, or allow for /ʁ X/ word internally < *h, *k cp. ''he, it'', Ger. ''hierher''), but an analogy for internal construction might suffice. Pragmatically speaking, the surface analysis is of course war + er (