I think it was more Voyager's general participation in events that threw off Annorax's calculations, not their temporal shields (though that does raise the interesting question of what happened to the Voyagers indigenous to the post-shields timelines. Did the little version of the Krenim ship see a pristine Voyager suddenly get replaced by a beat up one?). The temporally shielded bouys, by design, wouldn't have influenced anything, since they were hidden from everyone except the Prime-Universe Voyager (at least, that was the intention. Clearly they weren't as well-hidden as they thought). That was probably Janeway's insurance policy in case Voyager was destroyed or lost their temporal shields— the Voyager from the next timeline Annorax created would find the logs, and have a leg up.
Of course, at the end of YOH, there was no fancy calculations, trying to find the right beat of the butterfly's wings to get the exact result you wanted. Annorax's ship erased itself, and likewise erased its erasure of everything else. Simple and clean, with no probably percentages or counter-indications.
When the first temporal inversion wave hit Voyager and that small Krenim ship that intercepted them while Janeway was negotiating with the Zhaal, neither seemed to have known what was happening (at least that was the impression I got).
The Krenim ship was unprotected from changes in the timeline as was Voyager at the time, and the crews memories of both ships were altered.
For the captain on that Krenim ship, he was a captain of a large Krenim battleship now (and always was from his point of view - and he wouldn't be the wiser for it), and for Janeway and her crew, the encounter with the Zhaal never occurred, and the Krenim attacked them it would seem (as is evident by a banged up Voyager).
When Voyager developed temporal shields though and was hit by temporal inversion, they saw the Krenim battleship change into a small scout ship (similar to the one that initially intercepted them before they experienced the changes) - but the Voyager crew would have no way of knowing of the original encounter except theorising... neither would the Krenim for that matter (apart from Annorax).
Up until Voyager developed temporal shields, only Annorax and his crew were protected and knew what was happening.
I agree with the idea that the temporally shielded buoys would most likely not really affect anything... but I got the impression during the YOH episodes that it was the temporal shields that threw off Annorax's inversion.
Obviously, the ship's participation in various events would have to be taken into account... but Voyager hadn't done that much except running from the Krenim and sitting there when the wave hit them and interacted with the shields - which Obrist himself said was enough to throw off their calculations.
Hence I was wondering if the temporal shields on buoys would have done the same, possibly even helped reset the timeline... or, since they were hidden from everyone as you say, they merely survived the temporal reset without affecting anything else and sat there until they could be found - which begs the question, how the heck did the Krenim get access to the buoys and their logs so they could alter them for alternate Janeway?
Unless I missed that part in the novel.
Apart from that... we also know the temporal shockwave affected a given area, which might indicate that Janeway could have placed the buoys in places that she knew were outside the largest part of Krenim space which would play a part in buoys surviving the temporal reset and not affecting it.
