First, when you say "personal BSC," I am presuming that your organization already has a corporate BSC and has cascaded the BSC down through business units and is now cascading the BSC "to the desktop" by incorporating a "personal BSC" as a component of your individual performance plans. This would indicate that your BSC is fairly mature. However, if the organizational structure has been changing, a few questions come to mind: Are the business unit scorecards (that you are cascading off of in order to develop your personal scorecards) still valid? Was the restructure a result of the new strategy (in other words, was it done for the purpose of aligning the organization to better execute strategy)? Will the new reorganization hinder the organization's ability to effectively execute strategy?
In response to your primary question: "Does a changing organization hinder the BSC project?"....the answer is, it most certainly CAN put the project at risk. Engaged leadership is a critical foundational element of the BSC. If your organization is experiencing leadership changes, you run two primary risks to the BSC project: (1) you have a risk that new leadership will not support / use the BSC as a strategy execution tool, and (2) that the new leadership is not committed to the underlying strategic elements of your current BSC. Remember that the BSC is the mechanism to align the organization for the purpose of strategy execution. If new leadership is not supportive of the strategic elements, then your current BSC will be invalidated when the leadership sets course on a NEW direction. So in the case of new leadership, you may need to begin with leadership development because you cannot presume that the new leaders will know how to USE the BSC to lead the organization. You will then probably need to go through a re-validation of the strategic elements of your corporate scorecard (vision, mission, values, strategic themes, strategic objectives, strategy map, corporate performance measures, corporate strategic initiatives) to ensure that you have leadership buy-in to the corporate strategy.
Only then....after your new leaders are bought into the methodology, understand how to lead using the BSC, and have validated that the BSC reflects current strategic thinking....THEN you can confidently cascade down through the business units to the personal scorecards.
Your question also contains an element of organization change management. Simply stated, when an organization is in flux, the organization can suffer from poor morale, rumors and miscommunications, general mistrust, and people often become resistant to change of any sort. Under these circumstances, it is difficult to implement any type of project, including the BSC, because it represents a change from the status quo. We feel it is critical to build organization change management into every step of the BSC project and we systematically include change management techniques throughout our Nine-Steps-to-Success Framework.