Performance is poor as losses have increased and are projected to remain negative going forward as the company works through problem assets and realizes related expense.
Interestingly, the first instance of as stands for 'because'; while in the second instance it means 'while'.
Therefore, it is not a case of two instances in the same sentence. However, to avoid possible ambiguity, and more importantly, to improve readability, one of them would better to replaced with its synonym: it is certainly not advisable to use a word with radically different meanings in the same sentence, other than for creative/ poetic effect.
Performance is poor because/since losses have increased and are projected to remain negative going forward while the company works through problem assets and realizes related expense.