Zero-shot voice conversion (VC) aims to transform source speech into arbitrary unseen target voice while keeping the linguistic content unchanged. Recent VC methods have made significant progress, but semantic losses in the decoupling process as well as training-inference mismatch still hinder conversion performance. In this paper, we propose Vec-Tok-VC+, a novel prompt-based zero-shot VC model improved from Vec-Tok Codec, achieving voice conversion given only a 3s target speaker prompt. We design a residual-enhanced K-Means decoupler to enhance the semantic content extraction with a two-layer clustering process. Besides, we employ teacher-guided refinement to simulate the conversion process to eliminate the training-inference mismatch, forming a dual-mode training strategy. Furthermore, we design a multi-codebook progressive loss function to constrain the layer-wise output of the model from coarse to fine to improve speaker similarity and content accuracy. Objective and subjective evaluations demonstrate that Vec-Tok-VC+ outperforms the strong baselines in naturalness, intelligibility, and speaker similarity.