I don't think we know why DCIS persists after neoadjuvant therapy but is doesn't appear to affect outcome. Of course, with neoadjuvant therapy, the whole breast is excised so residual DCIS can't do any harm.
In the lumpectomy/ chemo/rads scenario - the known DCIS is excised, but some could still be present. However, DCIS is non-invasive and most DCIS never progresses. Follow up of breast cancer treated this way has shown very good disease free survival comparable to mastectomy with only a slightly greater risk of local recurrence (treatable with surgery.)
See the speculation below.
http://jco.ascopubs.org/content/25/19/2650.full
"It is biologically quite intriguing that DCIS, not unlike normal breast epithelium, often survives chemotherapy. Differences in proliferation rate cannot fully explain the greater chemotherapy resistance of in situ cancer because these lesions frequently have growth fractions higher than corresponding normal tissues and similar to that seen in invasive cancers.
26,
27 It is possible that physiologic resistance mechanisms that protect normal cells from cytotoxic insults remain more intact in in situ cancers compared with invasive tumors.
28 However, greater drug resistance of these tumors may be of limited clinical relevance because, by definition, in situ cancers do not metastasize."
Aussie Girl