Electronic healthcare records (EHR) contain a huge wealth of data that can support the prediction of clinical outcomes. EHR data is often stored and analysed using clinical codes (ICD10, SNOMED), however these can differ across registries and healthcare providers. Integrating data across systems involves mapping between different clinical ontologies requiring domain expertise, and at times resulting in data loss. To overcome this, code-agnostic models have been proposed. We assess the effectiveness of a code-agnostic representation approach on the task of long-term microvascular complication prediction for individuals living with Type 2 Diabetes. Our method encodes individual EHRs as text using fine-tuned, pretrained clinical language models. Leveraging large-scale EHR data from the UK, we employ a multi-label approach to simultaneously predict the risk of microvascular complications across 1-, 5-, and 10-year windows. We demonstrate that a code-agnostic approach outperforms a code-based model and illustrate that performance is better with longer prediction windows but is biased to the first occurring complication. Overall, we highlight that context length is vitally important for model performance. This study highlights the possibility of including data from across different clinical ontologies and is a starting point for generalisable clinical models.