When a paused plan resumes (either because the set number of periods have passed or you have resumed the plan manually), the invoices that occurred while the recurring plan was in a paused state will not be attempted. So, any missed payments will not be charged.
Once the paused plan resumes, the plan's next scheduled payment attempt will revert back to what the plan's recurring schedule was before the pause.
Examples:
1) A monthly plan was scheduled to be charged on the 15th of the month before you paused it. On January 1, you paused the plan for an indefinite period of time. On February 16, you resume the plan manually. The missed payments in January 15 and February 15 will not be attempted. The next scheduled payment attempt will now be March 15.
2) A monthly plan was scheduled to be charged on the 1st of the month before you paused it. On March 31, you paused the plan for 2 periods so that the plan wouldn't charge on April 1 or May 1. However, on April 2, you decide to resume the plan. The missed payment on April 1 will not be attempted. The next scheduled payment attempt will now be May 1.
3) A monthly plan was scheduled to be charged on the 5th of the month before you paused it. On September 4th, you paused the plan for 2 periods so that the plan wouldn't charge on September 5th or October 5th. If you take no further action, on October 6th, the plan will automatically move from a "Paused" state back to an "Active" state. The next scheduled payment attempt will be Nov. 1.