For measures that require timely action, the Meaningful Use Dashboard specifically counts whether or not the clinical action was taken during the corresponding timeframe, and doesn't require the encounter to be signed within the same timeframe. For example, in Stage 2 Objective 8, patients need to have access to view online, download and transmit their health information within 4 business days after the information is available to the provider. The encounter can be signed afterwards.
It is important to note that you will not receive credit for actions after your reporting period. For example, you cannot go back to a chart after the reporting period and select that a patient did not have any known allergies and receive credit for that action for Meaningful Use, even if the chart is from a visit that occurred during the reporting period.