When parsing a file, the coordinate system specified in the exchange file is taken. If no coordinate system is specified in the exchange file, the default coordinate system for the file format being opened is taken (see Settings→Options→Formats).
You can see which coordinate system (hereinafter - CS) is currently set for the exchange file by right-clicking on the tab of the exchange file and selecting "Set coordinate system". In the dialog that opens, you will see the current CS of the exchanged file. In the same dialog, you can change the CS set for the exchanged file (if for some reason the read or recognized CS is not correct). Note that if you change the CS through the "Set Coordinate System" dialog, this does not change the coordinate values recorded in the file. It only changes the coordinate system in which the coordinates specified in the exchange file will be processed.
It is easiest to check whether the CS selected for the file is correct by looking at the image of the file boundaries superimposed on google raster maps - as a rule, an incorrectly selected coordinate system gives an error of more than 100 km - this is easy to notice on google maps. The only exceptions are SK42 and USK2000. The difference between the coordinates of the same point differ by no more than 10m, and on average they differ by 2-3m. This is not always easy to see when overlaying borders on satellite images or maps.
After we have made sure that the correct coordinate system is selected for the file, it may be necessary to recalculate the file coordinates to another coordinate system. To do this, use the command "Generate exchange file in format..." (Right mouse button on the tab of the exchange file ...→Generate exchange file in format...) In the dialog that opens, you can not change the file format, the main thing is to check the box "Change coordinate system" and select the desired coordinate system. After pressing the OK button, the exchange file will be re-formed using the selected coordinate system.
A little about USK2000. For the correct conversion of the coordinate system based on the SK42 ellipsoid (and this is SK42, SK63, all the old local coordinate systems) into USK2000 (as well as all USK2000 - MSK), you must have a transformation field in the Ntv2 format (usually a file with the gsb extension). If you have such a field for your region, you can specify it in the program settings (see Settings→Options→General). If the file is not specified, the transformation field built into the program is used. The accuracy of this field is ~10 cm with respect to the official transformation field.