FITC reacts with primary amino groups (lysine and the N-terminus) of proteins, so the carboxylate groups (Asp, Glu and the C-terminus) are still free to react with EDC/NHS to form the NHS ester that can be used to react with the amino group of APTES.

I would be concerned about loss of biotin binding function and/or solubility of the avidin if it is excessively derivatized.

Another concern is derivatization of the carboxylate group of fluorescein (I don't know whether this aryl carboxylate reacts with EDC/NHS), which might quench its fluorescence.

What if ATTO - Avidin is used instead of FITC - Avidin.

I remember using fluorescein tagged biotin for my initial tests for EDC/NHS functionalized avidin. The fluorescence was quenched.

Also, thank you for reply. You have always been helpful :)

Again, it comes down to the chemistry of the dye. There are many ATTO dyes. Look up the structures. One place to see them is here:

https://www.atto-tec.com/fileadmin/user_upload/Katalog_Flyer_Support/Catalogue_2009_2010.pdf