Sampling and uncertainty of sampling are important tasks, when industrial processes are monitored. Missing values and unequal sources can cause problems in almost all industrial fields. One major problem is that during weekends samples may not be collected. On the other hand a composite sample may be collected during weekend. These systematically occurring missing values (gaps) will have an effect on the uncertainties of the measurements. Another type of missing values is random missing values. These random gaps are caused, for example, by instrument failures. Pierre Gy's sampling theory includes tools to evaluate all error components that are involved in sampling of heterogeneous materials. Variograms, introduced by Gy's sampling theory, have been developed to estimate the uncertainty of auto-correlated process measurements. Variographic experiments are utilized for estimating the variance for different sample selection strategies. The different sample selection strategies are random sampling, stratified random sampling and systematic sampling. In this paper both systematic and random gaps were estimated by using simulations and real process data. These process data were taken from bark boilers of pulp and paper mills (combustion processes). When systematic gaps were examined a linear interpolation was utilized. Also cases introducing composite sampling were studied. Aims of this paper are: (1) how reliable the variogram is to estimate the process variogram calculated from data with systematic gaps, (2) how the uncertainty of missing gap can be estimated in reporting time-averages of auto-correlated time series measurements. The results show that when systematic gaps were filled by linear interpolation only minor changes in the values of variogram were observed. The differences between the variograms were constantly smallest with composite samples. While estimating the effect of random gaps, the results show that for the non-periodic processes the stratified random sampling strategy gives more reliable results than systematic sampling strategy. Therefore stratified random sampling should be used while estimating the uncertainty of random gaps in reporting time-averages of auto-correlated time series measurements.