You have to deposit the Form 108 with Articleship period showing your total leaves.
Thereafter, they sent you letter for excess leave days and ask you to re-register yourself with any practicing CA.
After that, you submit the regn. form 103 & 102 with the no. of excess leave period (new articleship period) and completion of this you can submit Form 108. However, if you continue your articleship with the employer (from where original articleship period served) then you are required to submit Form 107 instead of Form 102.
You have to take this way,,, you can take other ways but you have to consider that Form 108 should be submitted within 30 days from the date of completion of period indicated in the Form, otherwise, charges would be collected by way of DD for the period of delays. (Same for Form 103).
Further, You can register immediately means without been waiting for the receipt of letter from ICAI, if you are sure of excess leave period. But, it is advisable Submit the Re-registration Form 103 after receipt of letter, in any case, so that alteration can easily be conducted.