This avreich is married to a previously divorced woman, which is now a problem as per his new discovery of his priestly status. A kohen is not allowed to marry a divorcee. Any children form a such a marriage would be chalalim, losing their kohen status, and he himself would be severely castigated and lose his kohen status in practice. It does not seem like a big deal as he never benefited from, or accepted the responsibility of, his kohanic status that he didnt even know about until now, but it is also a serious prohibition. 

the couple went to Rav Yitzchak Zilbershtein, rav of Ramat Elchonon neighborhood of Bnei Braq, for direction in how to proceed. Rav Zilbershtein instructed them to initially separate while the issue is clarified.

The issue was given to a beis din to clarify. They discovered that the young man's father was not religious and did not care enough to clarify his own status, nor did he ever tell his kids that they are of kohanic lineage.. The beis din discovered in their research that the form itself that was discovered of his father's marriage is not considered "eidus" to his kohen status according to most poskim, and even according got the poskim that it might be, the form had the father first listed as a regular Israelite and that was later crossed out and changed to kohen, so the form as testimony is worthless according to everybody. Additionally, that form of the father was only signed by one witness, not two, further invalidating it as testimony. Adding to this there is the general "safek" of today's kohanim with no documented lineage.

Based on the above, the beis din decided that this avreich could go back to living with his wife and his 6 children, with the status of a regular Israelite.