45 minutes ago, wn78 said:

The question is if a rejected visa could result in a red flag in your record in their immigration database....and then the flag pops up at the border next time you try to enter visa-exempt.... I guess no way to tell exactly how they have it setup, but it is a possibility.

There is no linkage between embassies and consulates with immigrations database.

1 hour ago, wn78 said:

Yes I understand there will be no mark in my passport if the e-visa is rejected.  But the passport is of little concern, after all you can always replace it.  The question is if a rejected visa could result in a red flag in your record in their immigration database....and then the flag pops up at the border next time you try to enter visa-exempt.... I guess no way to tell exactly how they have it setup, but it is a possibility.

You're overthinking this. If an IO you encounter really wants to deny you entry (unlikely based on your history in my opinion), he or she will find a reason, even make one up if necessary. That might or might not lead to an offer to resolve the situation, at a price. 

2 hours ago, wn78 said:

Yes I understand there will be no mark in my passport if the e-visa is rejected.  But the passport is of little concern, after all you can always replace it.  The question is if a rejected visa could result in a red flag in your record in their immigration database....and then the flag pops up at the border next time you try to enter visa-exempt.... I guess no way to tell exactly how they have it setup, but it is a possibility.

It is very unlikely that The Ministry of Foreign Affairs e-visa system and the Immigration Bureau's systems are linked in any way. Historically, they have been jealously protected separate fiefdoms.