I'm trying to fully understand the chronology of the stories collected in Batman: Second Chances. I know that Batman #408-409 are flashback issues, set before Legends. (Making them the second-ever Post-Crisis Batman flashback story). Are Batman #410-411 also set before Legends? I know that issues 402 and 403 are set after Legends.
As I have pointed out elsewhere there is evidence that Earth-Thirty-Two survived Crisis because it was a hypertime reality. In fact, hypertime addresses a lot of issues; conflicting statements regarding when a particular version of a character appeared and so on.
The point is that saying something happened before the Crisis (even if it is the Post-Crisis version of the Crisis) is nonsensical at best as we know that certain realties survived Crisis. Case in point is Batman: The Last Angel which despite coming out in 1994 was eventually assigned to Earth-Thirty-Two. This makes assigning flashback stories to Earth-One or New Earth iffy at best.
The problem is in 1987 (when Batman #410-411 came out) DC didn't really have a handle on how Crisis happened in the Post-Crisis DCU. For example, Post-Crisis Superman remembered meeting Earth-Prime Superboy during Crisis. (Superman (Volume 2) #8) which Post-Crisis should have been impossible.
More over all the issues you just cited are post Hypertime and therefore tell us next to nothing about the Post-Crisis (1986) Per-Zero Hour (1994) version of Crisis. Heck, Legends of the DC Universe: Crisis on Infinite Earths came out the same month hypertime was formally revealed (Feb 1999) and it recounted the Pre-Crisis version of Crisis.
If that wasn't enough during Zero Hour itself Brainiac 5 revealed that Pre-Crisis events had (somehow) happened in the post-Crisis continuity (Legionnaires #17) The end of Zero Hour wasn't any help as the timeline expressly stated that Crisis on Infinite Earths had happened 4 years ago and even showed five Earths. Then DC got the bright idea of implying that all those realities seen during Zero Hour actually existed as part of hypertime.