Interesting, I didn't knew the unit was counted as dead during the delay of waiting for reincarnation effect if I understood Ezekiel correctly.
Just keep track of units "dead" during reincarnation effect, for example in unit groups and periodic timer checks and it shouldn't be difficult at all to keep track. You need to make sure your system don't kick in when the unit dies and reincarnation cd is still present. DSG and Ezekiel has provided enough basic info you need to know.
Reincarnation ability sidenote:
As I made it in cruiser command where the crew is normal units, not heroes, I didn't base it on the reincarnation ability, I made a custom reincarnation ability (not cloned from reincarnation, but using a dummy ability) using timers and unitgroups, since normal units tend to often not leaving a corpse after death when the reincarnation cd hasn't finished and the crew in my map is not a hero type unit. (The original wc3 roc game was probably never originally designed reincarnations ability for normal units to have this ability in the first place and was never fixed in any later wc3 updates, its only really intended on heroes and works good for them since they don't leave a normal unit corpse in death)