So, I refunded my specialists to reassign them to a different sector/orbit between runs, but now everything costs 300 plus specialists to upgrade. I basically lost all my progress and made the game several orders of magnitude harder. This makes no sense.
Vexilius III is so overpowered that it's not even funny. Seems like your brilliant design skills got kinda rusty after your long hiatus. I would suggest that you tone down his passive, cause he's ruining draft atm (which is the only interesting part of the game - at least for me).
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Check the Multiplier button at the top of the screen when in the Specialist Map. It may be set to something else other than 1 phase per purchase.