You are correct, we match subject lines in absence of explicit headers. The matching window is the most recent 3000 messages. This was more important two decades ago when mail user agents were less fastidious with headers. Will think about it. Thanks for the feedback and sorry for the misthread. If this is causing trouble for others as well, please speak up now.
https://www.mail-archive.com/faq.html#threading https://www.mhonarc.org/MHonArc/doc/faq/threads.html
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