Well, you will be eligible to apply, but if you will be eligible for grant of ILR or not is a different matter.
To be honest, I am not very clued up about excessive periods of absense under the points based system. I just haven't got that much inclination to know about PBS, as at times its too muddled up. But I can certainly tell you that even if you do not qualify for grant of ILR, there is certainly nothing stopping you for getting an extension under tier 1, as long as you fulfill the requirements, and then apply for ILR at a later date.
I know many people who were granted with access absences, because work related absences are not regarded as absences. But your case has another dimension, that you were paid in India.
I would suggest that you contact an expert immigration advisor who specialises in PBS, and discuss your case. There may well be a good chance that you get ILR now without having to wait further.
I can recommend some very good advisors who know PBS inside out. search in google for MEDIVISAS, SKILLCLEAR and VISADIRECT.
Hope this helps.
