I played around a little with the
Chou-Wakusei Senki - MetaFight (J).nes ROM (GoodNES 3.14) after seeing that happen and will summarize some info here. Hopefully this will serve as a starting point for figuring out the glitch. I used FCEUX 2.2.3 and only played as far as the second boss fight.
After the scrolling ends when you enter a boss room, the following code is executed:
$971A:A5 14 LDA $0014
$971C:29 07 AND #$07
$971E:AA TAX
$971F:BD 2B B6 LDA $B62B,X
$9722:60 RTS
$9627:2D FB 03 AND $03FB <-- This is the important check
$962A:D0 0F BNE $963B <-- Branch taken if boss defeated
$962C:A9 C0 LDA #$C0
$962E:85 51 STA $0051
$9630:A9 08 LDA #$08
$9632:20 8C C1 JSR $C18C
$9635:20 CD 97 JSR $97CD
$9638:E6 46 INC $0046
$963A:60 RTS
$963B:20 1A 97 JSR $971A
$0014 is the value (current area - 1) at this point. At $B62B, you find a sequence of increasing powers of two, starting with 0x01. Per
Data Crystal's RAM map, $03FB indicates which bosses have been defeated. So this checks if the boss of the current area has been defeated. If it has but the item has not been obtained, then the item is displayed. That seems to be what happened during the race.
If the boss has not been defeated, then the room flashes, the boss loads (including its health), and you proceed with the fight. It appears that the health of the first two bosses is hard-coded into the ROM. For area 1, the pertinent code is:
$9C15:A9 80 LDA #$80
$9C17:85 53 STA $0053
For area 2, the pertinent code is:
$91FD:A9 40 LDA #$40
$91FF:85 53 STA $0053
The value from $0053 eventually ends up somewhere around $0470, but the exact RAM address varies. If you change the health to 0x00 before starting the fight (e.g., set execution breakpoint on $9C17, change A from 0x80 to 0x00, then continue emulation), the boss graphics load but immediately go into the death animation. This leads me to believe that whatever Skavenger did may have corrupted $03FB. There are likely other possibilities, but I will let someone with more time and experience take over.
Actually, one other thing. This is the code that is executed when a boss is defeated:
$971A:A5 14 LDA $0014
$971C:29 07 AND #$07
$971E:AA TAX
$971F:BD 2B B6 LDA $B62B,X
$9722:60 RTS
$97A7:0D FB 03 ORA $03FB
$97AA:8D FB 03 STA $03FB
Most if it should be familiar from that first block, but the last two lines update the value at $03FB rather than testing it.