Can you provide a source for this statement other than the release notes for SailfishOS 1.0.4 (discussed below)?
IMO this is “not true”.
What Jolla added to the GUI updater of SailfishOS 3.4.0, is listing all installed RPMs which have replaced “system RPMs” (i.e., ones from Jolla’s repositories) and recommending to uninstall them before upgrading. But that detection seems to be faulty, sometimes reporting many of Jolla’s own RPMs (i.e., “false positives”). In case of
libyaml-cpp0_6-0.6.2 (from openrepos-birdzhang), I suppose that people did not pay attention (or that this detection mechanism also yields “false negatives”, sometimes).
Note that beyond the functionality documented by Jolla, this mechanism also apparently disables (≠ “delete”) the repositories, which provide the detected “system-RPM replacing RPMs”; at least this is what I observed when upgrading from SailfishOS 3.4.0 to 4.0.1.
Furthermore, I believe to have read that Jolla implemented a “repository separation mechanism”, which was “enhanced” in some later SailfishOS release. But I have never seen the exact functionality described and fail to find the remark about the “enhancement” (but IIRC it did not state anything specific). Maybe this just addressed what has been introduced in SailfishOS 1.0.4 and the “enhancement” meant the aforementioned new functionality of the GUI updater of SailfishOS 3.4.0.
The statement from the release notes for SailfishOS 1.0.4 is, “We have implemented disabling of additional repositories before system updates with this release.”, but we all know and regularly see that this is not at all true / working this way: All “additional repositories” are enabled during an SailfishOS update, because their RPMs are also updated by a SailfishOS upgrade and before SailfishOS 3.4.0 “system-RPM replacing RPMs” were pulled in from “additional repositories”, if they carry higher version numbers that the ones provided by Jolla.
And one still needs to deactivate all open repos stuff before starting the upgrade?
Short answer: IMO “No” with any SailfishOS ≥ 1.0.4, if one strictly keeps repositories disabled which contain “system-RPM replacing RPMs” among other RPMs (e.g., openrepos-birdzhang, openrepos-nieldk, openrepos-lachs0r).
Repositories which deliberately and explicitly (i.e., its maintainer knows what he is doing and documented that) contain solely “system-RPM replacing RPMs” are O.K. (e.g., openrepos-obexdcontentfilterolf).