The GEDCOM standard allows for a date that is interpreted from another date.
The keyword "INT" indicates that what follows is the Gregorian DATE you've interpreted followed by the DATE_PHRASE you interpreted it from. The DATE_PHRASE is enclosed in parenthesis.
You should always translate the date the best you can to a Gregorian date, as that will be the calendar that you want your software to work with.
In addition, you should also always record the date in its original form. If the document gives the date as a Julian date or as a relative date, then that original form should make up the DATE_PHRASE. The DATE_PHRASE is any statement offered as a date and need not be recognizable to any date parsing algorithm, and it may be up to 35 characters.
e.g. The way to represent your example in GEDCOM with a relative date would be:
2 DATE INT 13 Jun 1649 (2. post trin. 1649)
With a Julian date it would be:
2 DATE INT 13 Jun 1649 (Julian date: 3 Jun 1649)
If your software supports this form of GEDCOM, then you will see a checkbox option to indicate that the date was interpreted and it will then let you enter the original phrase that it was interpreted from.
If your software doesn't have this option, then you can enter the original form of the date as a NOTE attached to the date, e.g.:
2 DATE 13 Jun 1649
3 NOTE Interpreted from relative date: 2. post trin. 1649
or
2 DATE 13 Jun 1649
3 NOTE Interpreted from Julian date: 3 Jun 1649
The NOTE method gets around the GEDCOM limitation of 35 characters for the interpreted date.
Whether or not your software supports interpreted dates in its GEDCOM, it would not be bad to choose to use the NOTE option all the time, since all software should support the latter.