Do I have to go through another 6 months of separation in order to obtain a divorce, if I was previously separated 3 years ago?

I really do not know what happened and it is best to actually look at al the documentation to give guidance here.  But here are the grounds for divorce in Illinois:

• natural impotence at the time of the marriage and continuing thereafter
• bigamy (also a ground for annulment)
• adultery
• wilfully desertion or absence from the petitioner for the space of one year
• habitual drunkenness for the space of 2 years
• gross and confirmed habits caused by the excessive use of addictive drugs for the space of 2 years
• threatening the life of the other by poison or other means showing malice
• extreme and repeated physical or mental cruelty
• conviction of a felony or other infamous crime
• infecting the other spouse with a communicable venereal disease.
• irreconcilable differences (this is a no-fault "ground")

The "no fault" ground requires that:

• the spouses have lived separate and apart for a continuous period in excess of 2 years [Illinois Courts have found that "separate and apart" does not necessarily mean separate housing; if the parties reside in the same household, they must live as if they were "separate and apart."]
• irreconcilable differences have caused the irretrievable breakdown of the marriage
• efforts at reconciliation have failed and further attempts at reconciliation would be impracticable and not in the best interests of the family.

If the spouses have lived separate and apart for a continuous period of not less than 6 months prior to entry of the divorce judgment, the 2-year living apart requirement may be waived if both parties stipulate in writing. After separation, any period during which the parties live together while attempting to reconcile and participating in marriage counseling, or under a written reconciliation agreement, will count towards the required separation period if the reconciliation fails. 

Seek legal help.