A couple questions that should have been asked sooner:

1. Which version of BG2EE are you playing?
2. Are you using any mods?

[Edit for clarity.]
"what mods you have, if any"
"have no mods".

The version is irrelevant to the OPs problem. The save is corrupt. Asking which patch makes no difference in these boards.

Are you certain theres no alternative............. I cant go back, I played good deal of out this game.

HELLO

Don't be a pest. This is a forum, not chat. Be patient.

As to your question, yes, I'm certain. It is very clear that your saved game is corrupt. I sent you down to the sewers via the console and not only could you not get out, but you said that the entire place is now inexplicably empty when there should still be the kobolds and rakshasas in residence. That is not a coincidence. The game is corrupt.

Would exporting the character be likely to also export the corruption?

Eventually, I did get in.

I deleted .SAV file and one more file from corrupted save and I manage to enter - with everything reset.

I think it is time to give up.

No, this is map corruption not character corruption. Exporting the character would only preserve the character, not the current game.
I don't know who gave you that idea, but it was never going to work. The .sav file is your entire area progression, so naturally everything reset. It was bad advice.