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Chemically exfoliated nanoscale few-layer thin Li$_x$CoO$_2$ samples are studied as function of annealing at various temperatures, using transmission electron microscopy (TEM) and Electron Energy Loss Spectroscopies (EELS), probing the O-K, Co-L$_{2,3}$ spectra along with low energy interband transitions. These spectra are compared with first-principles DFT calculations of -Im$[\varepsilon^{-1}(q,ω)]$ and O-2p Partial Densities of States weighted by dipole matrix elements with the core wavefunction and including the O-1s core-hole and with known trends of the L$_2$/L$_3$ peak ratio to average Co valence. Trends in these spectra under the annealing procedures are established and correlated with the structural phase changes observed from diffraction TEM and High Resolution TEM images. The results are also correlated with conductivity measurements on samples subjected to the same annealing procedures. A gradual disordering of the Li and Co cations in the lattice is observed starting from a slight distortion of the pure LiCoO$_2$ $R\bar{3}m$ to $C2/m$ due to the lower Li content, followed by a $P2/m$ phase forming at 200$^o$C indicative of Li-vacancy ordering, formation of a spinel type $Fd\bar{3}m$ phase around 250$^o$C and ultimately a rocksalt type $Fm\bar{3}m$ phase above 350$^o$C. This disordering leads to a lowering of the band gap as established by low energy EELS. The O-K spectra of the rocksalt phase are only reproduced by a calculation for pure CoO and not for a model with random distribution of Li and Co. This indicates that there may be a loss of Li from the rocksalt regions of the sample at these higher temperatures. The conductivity measurements indicate a gradual drop in conductivity above 200$^o$C, which is clearly related to the more Li-Co interdiffused phases, in which a low-spin electronic structure is no longer valid and stronger correlation effects are expected.