Most judges I've seen return exhibits at the end of a criminal trial. If a problem arose, I strongly suggest you contact a lawyer and do not use a public forum, such as this, to detail your issues.
I almost every case I have seen in the District Court, the exhibits are returned to the parties by the court. Because there is a de novo appeal, if the matter goes to the Circuit Court, that party would have the obligation to admit the documents again. In the Circuit Court, by contrast, everything is retained by the clerk. The issue is the nature of a de novo appeal. Since everything is "starting over" it is in each party's interest to preserve the exhibits. If they can't, it will come back to haunt them in the second trial. There is nothing unusual about this. Additionally, even if the documents remained in the file, on appeal the proponant of the evidence still needs to meet all the evidentiary requirements to admit the evidence.
Please understand, without forming an attorney/client relationship this office is not providing legal advice. We are simply providing general information which should not be acted upon without careful consideration and the assistance of an experienced attorney.