And she had it somewhat easy
because Maximilian as second son had no real standing with his brother. The emperor was horrified by his liberal ideas. Only when FJ urged his brother to renounce his rights to the Austrian throne did he waver a bit, realising the hopelessness of the situation. The point of no return.
The one really warning them was Charlotte's grandmother Maria Amalia.
Maria Amalia was Charlotte's maternal grandmother?
Yes, she had some experience with the Bonapartes and distrusted them. Her mother Maria Carolina of Austria (herself a daughter of Maria Theresia and the one most resembling her in character) was an ardent enemy of Napoleon I. (who apparently labeled her the most generous woman of Europe) and distrusted the French as a whole, since they killed her sister.
With her brother Leopold II. they arranged some marriages between there children, amoung them her daughter Maria Teresa and the future Emperor Franz I/II. To make matters worse, it was her granddaughter Marie Louise (the first from this marriage), who would become Napoleon's second wife.
MA was born in 1782 and had to flee Naples with her parents and siblings from Napoleon. The tumour years didn't end until after Waterloo (which Maria Carolina sadly didn't see. She died in 1814, still being active during the Viennese Congress).
Interesting enough there have been rumours ever since that Maximilian was in reality the son of the Duke of Reichstadt. It's a pretty baseless rumour, coming from the fact that little Napoleon was pretty lonely at the Viennese court, but liked to spend time with the young Archduchess Sophie...
Luckily dying in 1866, Maria Amalia didn't see the disastrous end of the Mexican adventure...unlike Maximilian's poor mother, who also happen to be not very overjoyed by her son's plans.