Why did lincoln only free slaves in the states that were in rebellion and not all of the salves throughout the country

 Lincoln was wanting to retain the support of some states which allowed slavery but were loyal to the Union.

Historical context/details:

President Abraham Lincoln issued The Emancipation Proclamation as an executive order on January 1, 1863. The executive order declared freedom for slaves in  ten Confederate states in rebellion against the Union.  It also allowed that freed slaves could join the Union Army to fight for the cause of reuniting the nation and ending slavery.  

While Lincoln personally was strongly against slavery, he had to tread carefully in his role as president and commander-in-chief.  The Emancipation Proclamation was carefully worded in order to retain the support of four border slave states, which remained in the Union though they were states that permitted slavery, were  Maryland, Missouri, Delaware, and Kentucky.   Lincoln wanted to keep those states loyal to the Union cause.

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