In theory it's possible, but in practice it's very difficult.
Literal
Theory-above [topic-は] it [topic-は] possible [but-けれど] actually [topic-は] very difficult.
理論上は (in theory/theoretically) contrasts with 実際には (in practice/actually). 可能だけれど…難しい sets up a classic theory-vs-practice tension. The triple は (理論上は、それは、実際には) manages three different topics.