The discovery of O I atoms and C II ions in the upper atmosphere of HD 209458b, made with the Hubble Space Telescope Imaging Spectrograph (STIS) using the G140L grating, showed that these heavy species fill an area comparable to the planet's Roche lobe. The derived similar to 10% transit absorption depths require super-thermal processes and/or supersolar abundances. From subsequent Cosmic Origins Spectrograph (COS) observations, C II absorption was reported with tentative velocity signatures, and absorption by Si III ions was also claimed in disagreement with a negative STIS G140L detection. Here, we revisit the COS data set showing a severe limitation in the published results from having contrasted the in-transit spectrum against a stellar spectrum averaged from separate observations, at planetary phases 0.27, 0.72, and 0.49. We find variable stellar Si III and C II emissions that were significantly depressed not only during transit but also at phase 0.27 compared to phases 0.72 and 0.49. Their respective off-transit 7.5% and 3.1% flux variations are large compared to their reported 8.2 +/- 1.4% and 7.8 +/- 1.3% transit absorptions. Significant variations also appear in the stellar line shapes, questioning reported velocity signatures. We furthermore present archive STIS G140M transit data consistent with no Si III absorption, with a negative result of 1.7 +/- 18.7 including similar to 15% variability. Silicon may still be present at lower ionization states, in parallel with the recent detection of extended magnesium, as Mg I atoms. In this frame, the firm detection of O I and C II implying solar or supersolar abundances contradicts the recent inference of potential 20-125x subsolar metallicity for HD 209458b.
