Navigate to the desktop launcher / menu entry, open the launcher properties dialog for google chrome.

It should look like this:

/usr/bin/google-chrome %U

To make the flags that you want permanent, modify it to something like:

/usr/bin/google-chrome --allow-file-access-from-files

You may also need to delete and re-pin your icon launchers after modifying it. Chrome should launch with the specified flags enabled after the modification.

Alternatively, you can simply create a new launcher with the above and use it to start chrome.

To check if the flags that you modified are being loaded:

$ cat ~/.config/google-chrome/Local State

and scroll up to the block entitled

"session_restore"

Your flags should be listed in the block, before

--flag-switches-begin --flag-switches-end.

Opening chrome and navigating to the URL

chrome://version/

should also list enabled flags in the

Command Line 

block

This is a list of the google-chrome / chromium flags:

http://peter.sh/experiments/chromium-command-line-switches/