Low ion Abundances on samples, normal tune file

There are two columns configured to the Back inlet.  This will cause issues.  Fix the column configurations.  For optimal results both columns should be running in  Constant Flow mode. 1.2 ml/min of helium is optimum for the MSD.

There are a number of differences between the before and after methods.

The oven program changed, before was 4 °C/min to 276 °C and now it's to 270 °C

Many of the injector parameters are different. Solvent A washes, solvent A volume, Solvent B volume Sample wash volume.  Doing any washes with less than a fully syringe requires the use of a PTFE tipped plunger in the syringe to reduce premature wear.  This is stated in the sampler manuals.

ALWAYS use viscosity delay of 2 seconds or more.

The inlet pressure and flow parameters are different.  It is critical to have sufficient flow in the inlet.  Gas saver 20 ml/min is marginal with high final oven temperatures, like your 290 °C.  Please increase gas saver to 30 ml/min.  Also - purge flow to split vent 15 ml/min does not sweep the ~1 ml volume liner quickly enough to remove any solvent residue in the liner.  Increase that flow to 50 ml/min or more.

The transferline before was 280 °C and now is 230 °C.

The EMV is different, probably due to tuning.   Your GCMS Serial Number US83140737 is a 5975C - TAD Inert XL EI/CI MSD ...from October 2008.   Has the electron multiplier, a consumable part, ever been replaced?  Have the ion source insulators been replaced?  If the lenses have been cleaned multiple times per year for almost fifteen years then the entire ion source may need to be replaced, too, depending on how hard you clean and with what method.  See: (+) GCMS Ion Source Cleaning - Videos - GC/MS Portal - Agilent Community

Is the system still using a Pfeiffer MVP-070-C reciprocating rough pump?  Has it been replaced ever?  

If two columns are configured to one injection port, the diagram on the GC driver page shows it.  

If you click on the ellipses after the tune file name, a tune file selection window opens.

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Thank you for pointing out these questions. We will try to change these parameters accordingly.