updating theme

I have an E-commerce website and for this site i have bundle of custom scripts in my function.php, header.php and footer and other than this i have some custom js scriptsin my theme assets folder. Previously when ever an update comes i would just replace the new function.php with older one but now if i do so i get fatal error can you please guide me to update my theme properly and incorporate those changes with new version …
Any suggestions are welcome….
thanks in advance for your reply…!
cheers…

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