It is very ddifficult to interpret this phrase.
時間の風 is the word made by Yoshiki,It's not usual Japanese
So We have to guess his emotion and felling.
This is my interpretation,other people may interpret diffarent way.
流れる涙を 時間の風に重ねて
I had been crying with passage of time.
時の風 passage of time.
(流れる涙に)重ねて with,together