I guess you'll have to tell us how you did this in BLS, and if your center uses BLS-2016 A/S. You've been around CDE products longer than I have.
In a test league (I used a 24-team league because I had a dummy league in my library, and I made the change in week 1 because I hadn't used this dummy league for any scores yet) I changed the lane assignment as follows:
Under Setup > Lane Assignments, with the week 1 date highlighted, I clicked on the number "9" in the dark blue lane numbers at the top, which brought up a dialog. For this, I changed 9&10 to be on 25&26, the next available pair in my case. I then checked "this week only" and clicked "OK". After this, since the change affected everything to the right of 9&10, I clicked on the "27" (which had previously been "11") and, using the same procedure as above, changed 27&28 back to 11&12 so that only 9&10 were moved to a vacant pair.
Entering random scores and absentees, and generating a standings which displays two weeks' of assignments, I saw that week 2 went back to 9&10 as would be expected and I did not duplicate the error that you saw, but I do not use an A/S version of BLS.
Now, with no scores entered for week 1, the lane assignments had separate grids, and by that I mean that since in that case week 1 hadn't been bowled yet, the standings showed that 9&10 had been moved to 25&26, but in week 2 it had a separate grid of lane numbers that had 9&10 where it belonged. I can attach images showing what I'm describing if it would help, although it may take me a little time to reply given my vacation status (I'll have my laptop with me).
You don't mention if this league is interfaced with or uses a BLS Autoscoring system, and it's entirely possible that if scores (and with that, lane numbers bowled) were exported back to BLS, that may have been something that BLS couldn't correct and displayed that incorrectly as you mentioned. I have never used an A/S version of BLS, but that's the only thing I can think of.
Always check, download, and install the most recent update of your software to ensure that issues may have been corrected.