Hey Zaher,
The reason why it happens is because the sub-basin or hru level parameter that you are describing in the parameter text file doesn't exist in the project. Some reasons for this is:
1. your format in your text file may have a mistake
2. the parameter you are trying to change may not exist at the level you are trying to change at (i.e., you can't change a basin wide parameter at an hru level) - to know what level each parameter operates at you can check your swat2009 access database in the "autoinpar" table. The column "type" specifies at what level each parameter operates at:
1 = basin-level parameter 2 = subbasin-level parameter 3 = hru-level parameter 4 = crop-level parameter
3. (what my problem was) If you are trying to change parameters at the hru level, the format asks you to sepcify the parameter, landuse, slope, and soil "texture" , not soil name. I was using custom soils and had not filled in anything for soil texture since it was optional and was not necessary to run the project in arcswat. What I ended up doing is that I gave each soil a unique arbitrary soil texture so that it can be used to differentiate hrus. You have to do this in your swat2009 access database in the usersoil table.
4. Even after you do all this, you might still get a few files unchanged when changing parameters at the hru level. This is because these hrus may have been removed as a result of HRU definition that you have done in the arcswat project.
I hope this helps. If you don't figure it out you can upload your par_inf.txt and I can see if I can spot any mistakes.
Cheers,
Yuestas.
Upload your par_inf.txt file here.