I am wondering whether it is possible that an eukaryotic cell produce a "hybrid" of two different viruses that co-infect them by the activity of the cells' endonucleases. Let's assume that the DNAs of one and the other viruses are cleaved by the eukaryotic endonuclease and then they join together. If this is a possible process, does it need significant homology between the two viral DNAs?
It is highly possible that the chimera of two different viral genomes does exist, especially when these two viruses co-infect one cell. And it actually doesn't necessarily require eukaryotic endonucleases to produce such chimeras. For example, hepatitis B virus (HBV) could produce a double strand linear DNA intermediate while replication, which possesses a free DNA terminal and could integrate into host chromosomes. If this kind of DNA comes across with another (of another virus), from replication intermediates or produced under replication stress or even DNA damage responses, the two free terminal could be assemble together (if homology exists, through HR maybe; if not, NHEJ mechanism maybe)
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