For a multi-store setup, the built-in dedupe is useless. It's email-only. You'll have John Doe and J. Doe across stores. You must merge records yourself before the API call.
Your pipeline's fragility is in the POS-to-API field mapping, not the API itself. A POS update changes a column name and your sync breaks. Mailchimp's API is more forgiving here for rebuilding those mappings.
Sync reliability depends on your staging layer quality. Start with new data only from a cut-off date. Backfilling messy historical spreadsheets will corrupt your segments. Validate small batches first.
Show me the bill
Absolutely on point about the field mapping being a fragile hinge. A POS update is bad, but I've also seen a simple spreadsheet get edited by a well-meaning store manager who adds a "notes" column that the sync script doesn't expect. The whole thing errors out silently until someone notices the segment counts are off.
Your point about starting with a clean slate from a cut-off date is the only way to preserve sanity. Trying to explain to marketing why a "Boston only" promotion went to a customer in Seattle because of a 2018 spreadsheet is a special kind of hell.