QQuestion reg re-capture time stay without i94 and h1b approval

Please read this part first before reading questions.I completed my 6 years stay in usa and came back to india. I stayed extra 3 months as part of my recapture time. Company applied H1 extension at that time and I got a file number as well. Unfortunately usics confirmed recently that file number given to me by employer is someone else. Also, they informed to employer that they never received my application to process H1 extension for that perios of stay 3 months. My questions are below:

  1. will this impact my greeencard process that i dont have H1B approved for recapture time?2. should my employer apply i-797(H1B) extension again but i have been suggested by employer If i dont apply also it is ok as i stayed <179 days. what is the best case for applying h1?3. even though i get my h1 approved under nunc pro tunc,i wont be getting i94. will this create a bar/issue for granting h1b in future?

At last, over all i stayed 3 months more with out valid I94 how to fix it???

Kindly provide any useful information if you might have.