Mr. Srivastava,
When you have paid a certain amount as salary for 3 years, it becomes defacto the normal salary. It is not the duty of the employee to come and report an excess in the salary so long as the salary slip matches the amount of salary received. Specially not if everyone else or a certain group definately, got similar excesses.
No court or labour officer is going to allow you to recover the amount paid for 3 years from the concerned workers. It is only logical.
Recovery by adjusting against future rise (if the union agrees, that is) would not give rise to any accounting problems. Why should it ? The entry for salary or anything else is not being affected. The quantum of salary being paid in future does not go up at the rate it was expected to. Why should that affect accounts ?
And what are you planning to tell the pf department ? I made a mistake and paid more pf because I paid a higher salary to workers. Now give me the money back with interest. I would like to witness the reaction of the concerned officer :)
If you want to engineer a strike in your factory, then by all means, go ahead and give notice of recovery from the workers.