
In agreement with some Gurus: http://www.warnercon.com/articles/Article%209%20-%20Handling%20Out-of-Sequence%20Progress.pdf
In agreement with other Gurus: http://www.htcprojectcontrols.com/SB002.pdf
"It is important to note that Retained Logic or Progress Override affects a schedule only if one or more activities with the conventional Finish-to-Start ties show out-of-sequence progress"
The above statement refers to P3 but maybe there is a possibility it also holds on P6. Therefore if the out-of-sequence is due to other relationship type such as F-F neither Progress Override nor Retained Logic rules as defined by the software will be applied. Still those occurrences shall be resolved.
Take a look at the following schedule; Activity 2 finish should finish before Activity 1 finish but it did not happened, it will allow Activity 3 to start before finish of Activity 1 breaking the required links sequence of finish Activity 1 ==> finish Activity 2 and then you can start Activity 3.

Yes broken links does not necessarily only affect connected activities but others in the sequence might be affected as well. As you can see there is much controversy on which one is best, Retained Logic or Progress Override, but there is agreement none is a sure bet. Make sure you can filter for broken links, even from prior updates as there might be active links that might still be affected.
Another reason to keep valid the updated schedule links is that in order for contemporaneous analysis be valid the updates shall be performed on the run, not latter. The Contemporaneous Method hinges on the principle that in order to determine the impact of delaying events, the status of the project must be established at the time those events occurred. In essence, the schedule needs, first, to be updated at the time of the delay and, second, to be updated to incorporate any planning changes to coincide with the contractor’s plan for pursuing the work.
If your software allows for some constraint types such as mandatory finish constraints that can create impossible schedules make sure it can identify the out-of-sequence events caused by such constraints, many such software cannot identify the occurrence.