QB Issue Resolution:

 Is it possible that you put them in the wrong bank account? When you go to banking make deposit, are they there? If you enter the payments and made the deposits then I would look in other checking or savings accounts to see if they were deposited there.

Resolution for Issue 'Reconciliation. The checks are shown as received but I don’t have any acknowlegement of deposit. All deposits from March 15th through May 6th 2016 are missing.' available: Yes (Solved).
Source: Intuit Community forum.

Reconciliation. The checks are shown as received but I don’t have any acknowlegement of deposit. All deposits from March 15th through May 6th 2016 are missing.: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

Support for acknowlegement
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Error Recovery for acknowlegement [Canada]
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