The Problem
Most designations, including the imperial capital but conspicuously excluding "autonomous", have the imperial administration structure core.sectorImperialAdministration that grants administrtechLevelAdj: {value:5.0 op:min}. This causes the planets to increase to TL5 if lower and raises them back to this level if they drop below due to resource shortages, etc.
Sector capitals have a different administration structure, core.sectorCapitalAdministration, which does not include administrtechLevelAdj. If a planet is above TL5 but is in the process of regressing to a lower fatedTL when it gets designated as a sector capital, I believe it can drop below TL5.
A Solution
Add administrtechLevelAdj: {value:5.0 op:min} to core.sectorImperialAdministration. Part of an active pull request.
Included in pull request 4.
Should be resolved, reopen if it is seen to recur.