All genomic dna is broken up to some degree but many of the broken fragments are so large that they are all running at the size limit of the gel so appear to be a band. Much of the smearing that you can see is hugely longer than the region that you are sequencing and the shearing ,if mechanical, will be randomly distributed so I would expect good results from high molecular weight smeared dna
We described a single multi-purpose PCR-based integrity assay for both native and bisulfite treated DNA (doi.org/10.1101/168195). By comparing the results of both assays you will have an idea about the effect (depends on the quality of your native DNA and the way you performed the bisulfite treatment). Works for most investigated mammal species (assay design strategy can be used for other species classes). In addition we described ""An optimized strategy for cloning-based locus-specific bisulfite sequencing PCR" (doi.org/10.1101/239566). Don't hesitate to contact me for feedback.
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