Thanks for your input everyone. I spoke to my accountant who advised not to issue a tax receipt. He said I would essentially be issuing a completely different receipt which would artificially create more income for myself, and could trigger an audit for me.

Also, according to the CRA rules regarding child care expenses and separation, I don't think dad would be eligible to claim the expenses anyway. I took this snippet off the CRA website: "If, in the year of separation, reconciliation does not occur within 60 days after the end of the year, there will not be a supporting person for the year. In this case, child care expenses will be allowed only to the individual who resided with the eligible child and only to the extent that the expenses were paid by that individual to enable the individual to engage in one of the activities listed in ¶1.9"