Checked cawiki wmf.10 and summarized the findings for various test users in the table below. Some of the factors affecting the User talk page state could be

• previous switching between different formats (Structured discussions and wikitext)
• enabling/disabling the Discussion Tools option; or whether the Discussion Tools were enabled by default on a wiki

Limitations of testing - (1) was not tested on sufficiently big Flow boards (2) very often disabling/enabling Flow was done several times (3) enabling/disabling of Discussion Tools was also done several times (for testing purposes)

However, in the table there are good example (and bad examples, marked in pink) when the disabling Structured Discussion went smoothly (Beta features preferences reflect the actual User talk page state and proper links are left on the page). As with many features related to Structured Discussion, probably each incorrect case could be treated on a case-per-case base.
@Trizek-WMF - you may check the link in the table, so to make sure that disabling Flow (for good cases) went exactly as it was expected.

Thank you for checking @Etonkovidova. So we have many possible cases. The case for Zilant63 is what was reported by two users at fr:wikisource, which led to this report.

Side note: Discussion Tools aren't part of the requirement, as they are the new default. The Beta option for DT is only for DT's new improvements, while some DT features are now the default (reply button, subscribe link...).

Since we have Editing team handling Flow Migration. I'll tag @VPuffetMichel to follow up on this discussion.