Thanks for the reply @pgr 
Well for favs that would be:
“public_html/themes/SuiteP/tpls/_headerModuleList.tpl”
For the TinyMCE it would be the css files that controls height etc. of the editor window and increase the number of pixels.
(I just cannot remember then by name since its a while I did it.)
The post marked as “Solution” in this thread we’re in has the answer you need.
Right, but how do you save these other customizations that I listed above then?
You mean the compose View js? I just redo them every time an upgrade touches that file.
Yes it is quite inconvenient and error-prone.
Sometimes I try to make the core change minor (say, adding or changing an incude) so that then I keep the bulk of my changes in some files outside core.
But that file is particularly large and ever-changing, it’s a mess to keep up with. Sigh…
Well no, sorry if I did not explain myself clearly. My apologies.
I meant 1.) the favs customization ( _headerModuleList.tpl) and 2.) the CSS files you need to modify in the theme so you can have larger writing window in TinyMCE when sending emails.
To make the Favorites + Recently Viewed customization upgrade-safe, save the changed file to: custom/themes/SuiteP/tpls/_headerModuleList.tpl
… as was already written in the answer marked as Solution above 
Thank you so much! 
2.) the CSS files you need to modify in the theme so you can have larger writing window in TinyMCE when sending emails.
If you wish this larger (or resizeable) email writing window change to be made upgrade-safe, you could submit a pull request with your updated code, to the github repo.
Thank you very much Chris!
