[We command all] Ministers of the so called reformed religion, who do not choose to become converts and to embrace the catholic, apostolic, and roman religion, to leave our kingdom
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Ministers of the so called reformed religion
These are ministers (priests / pastors / religious leaders) of 'protestant' Christianity.
who do not choose to become converts
To 'convert' is to abandon one religion for another. A 'convert' is one who has completed the act of conversion.
embrace the catholic, apostolic, and roman religion
The new religion is that of the Roman-Catholic church. 'Apostolic' refers to the apostles.
to leave our kingdom
Those who refuse to change religions must leave the country.
To expand a bit on "so called reformed religion"
Nowadays, we would hyphenate "so-called". This is used as a disrespectful term, ridiculing the opponent by implying "You might call it that, but we don't!"
The writer might have used "so-called" to mean
1) so-called reformed [religion] In this sense, it implies that the writer thinks Protestant religion is not really "reformed".
2) so-called [reformed religion]
More likely it is meant in this sense; from a Catholic point of view (at least at that point in history, and to some degree even today), any "reformation of Catholicism" is impossible because it is not faithful to the "apostolic" traditon.
3) so-called [reformed] religion
in this third sense, the writer would be scoffing even more at all Protestant sects, referring to them as if they were not "religion" at all.
You can find much more about these viewpoints on the Christianity Stackexchange.