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This paper discusses the problem of controlling a timed Petri net whose marking cannot be measured but is estimated using an observer. The control objective is that of enforcing a set of generalized mutual exclusion constraints (GMEC) and all transitions are assumed to be controllable. We show that the use of marking estimates may significantly reduce the performance of the closed-loop system and in particular may lead to a deadlock. First, we present a linear algebraic characterization of deadlock markings based on siphon analysis. Second, we show how this characterization may be used to derive a procedure that may be invoked to recover from a controller induced deadlock. Finally, we assume that the timing delays associated to transitions are known and show how this knowledge can be used to improve the marking estimate and to recover the net from partial deadlocks. This procedure is similar to the one used for deadlock recovery and may be invoked whenever a transition has not fired for a time longer than its expected delay.