It is good that the question -- were African Americans free during the period of Reconstruction -- offers the qualifier that the answer need not be absolute, because the answer is not absolute. While the slaves were indeed officially freed by President Lincoln's Executive Order, the Emancipation Proclamation, the effect of which was codified by ratification of the Thirteenth Amendment to the United States Constitution ("Neither slavery nor involuntary servitude, except as a punishment for crime whereof the party shall have been duly convicted, shall exist within the United States, or any place subject to their jurisdiction"), the institution of slavery continued to exist in spirit if not in law. This mainly happened through a form of indentured servitude, in which the ability of African American families that were formerly enslaved continued to be tied to their former owners through quasi-legal but always immoral arrangements by which the former could conduct subsistence agricultural activities on land owned by the latter. These former slaves had to be able to provide for themselves and for their families, but the legacy of slavery deprived them of the means to do so. Consequently, they remained dependent upon their former owners for land upon which to farm.
In addition to those arrangements, blacks would not be completely free until the the middle of the 20th Century, with the 1954 U.S. Supreme Court decision in Brown v. Board of Education, and with passage of the Voting Rights Act of 1965, both of which were needed to eliminate once and for all the institution of racism that had, post-Civil War, enabled southern states to practice segregationist policies that effectively deprived blacks of their civil rights as American citizens. While these developments occurred well-after the period of Reconstruction had effectively ended, the racist policies and practices of the South that emerged out of its defeat in the Civil War laid the foundation for the continued deprivation of human rights for African American citizens in direct contravention to the spirit and the letter of the Constitution.
African Americans were not enslaved during Reconstruction. However, they were not truly free in most times and places because they lacked economic power and political equality.
Of course, African Americans were legally free during Reconstruction. In addition, there were times and states in which they were able to vote and to hold office. However, this did not last long. White Southerners soon began to roll back African American rights. This was done partly through violence on the part of groups like the KKK.
Importantly, African Americans were not economically free either. They did not get the “forty acres and a mule” that they had hoped for. This meant that most African Americans were indebted to white landowners. This severely curtailed their actual freedom as well.
African Americans, then, were legally free, but did not enjoy true freedom during this time.
After the Civil War slavery was abolished and the South "slain" African Americans who were former slaves were free in all legal sense of the word.
However, while the Fifteenth amendment gave them rights as citizens (Wiki, Fifteenth Amendment of the United States Constitution) they were still looked at through the same lens of racism that had been aimed at them from before. Shortly after the Civil War the former Confederate soldiers were forced to re-swear their oaths and swear "Dog Oaths" to the new Union which did not sit well with the former soldiers. This led to riots in the deep South and the formation of new groups such as the Ku Klux Klan in Tennessee. It is often said that the South won the "2nd Civil War" or the Reconstruction era.
When it came time to grant the former slaves voting rights and privileges as citizens even Northern Republican lawmakers were hesitant to grant them full legal rights. They could still hold no office and no place in the country beyond very liberal states fully welcomed them as now equal brethren.
It is one thing to be considered legally free however these former slaves were held down by their old shackles of hate and racism that continued to keep them from having a fully prosperous future. In this way they were far from "Free" like their White counterparts were.