We believe Archanphel knows exactly who Apollyon is, and he doesn't seem too happy with his current actions. And Takaya has given us a lot of clues. The majority opinion is that Apollyon is
. It's probably also why he singled out Tetsuro and Mizuky.
Well, they didn't seem to salvage any of Guyver II's control medal, only some of the bio material. The stuff that needs the control medal to be controlled. If you pay close attention, her control medal is actually made of a different material than Guyver 1 or 3's. That is because it is an Alien metal that they could not reproduce at all, and seems to be the main reason that Valkyrie is having issues ( also it has been noted that Apollyon's armor IS made of the same metal as the Guyver control medal)
Valkyrie is actually the adopted sister of Oswald Lisker. And Liskers family is similar to the Makashima family in that they are long time Chronos supporters, thus the children usually join as well. She joined Chronos of her own free will and become an inspector like her elder brother under her own power. So she had made quite the name for herself, and like Lisker, was probably in good position to be a leader somewhere in Chronos. But Valkyrie has become a traitor to Chronos officially when she stole the proto-type Guyver unit that they had created. She only joined Guyot for 2 major reasons: 1. Keep Chronos off her back. They have been able to track her and try to capture/kil her. Guyot saved her from one such attack and offered his help with the next point: Revenge against Guyver 1.
So, she was "Helping" Guyot to get to Guyver 1 (the attack on the mansion was to try and capture Tetsuro and Mizuky)... But after their recent "loss" at the mansion, Apollyon and Guyver 1 nearly killing Guyot, and Agito fighting the rogues, I doubt their alliance will last much longer.